test_SeqIO
Testing reading sff format file Roche/E3MFGYR02_random_10_reads.sff
 ID and Name='E3MFGYR02JWQ7T',
 Seq='tcagGGTCTACATGTTGGTTAACCCGTACTGATTTGAATT...GGGCTTa', length=265
 ID and Name='E3MFGYR02JA6IL',
 Seq='tcagTTTTTTTTGGAAAGGAAAACGGACGTACTCATAGAT...AAATGcc', length=271
 ID and Name='E3MFGYR02JHD4H',
 Seq='tcagAAAGACAAGTGGTATCAACGCAGAGTGGCCATTACG...gagaacg', length=310
 ...
 ID and Name='E3MFGYR02F7Z7G',
 Seq='tcagAATCATCCACTTTTTAACGTTTTGTTTTGTTCATCT...nnnnnnn', length=219
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading clustal format file Clustalw/cw02.aln
 ID = 'gi|4959044|gb|AAD34209.1|AF069', Name='<unknown name>',
 Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=601
 ID = 'gi|671626|emb|CAA85685.1|', Name='<unknown name>',
 Seq='---------MSPQTETKASVGFKAGVKEYKLTYYTPEYET...PAMD---', length=601
Testing reading clustal format file Clustalw/cw02.aln as an alignment
 M- alignment column 0
 E- alignment column 1
 N- alignment column 2
 S- alignment column 3
 D- alignment column 4
 || ...
 V- alignment column 600
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|671626|emb|CAA85685.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading clustal format file Clustalw/opuntia.aln
 ID = 'gi|6273285|gb|AF191659.1|AF191', Name='<unknown name>',
 Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
 ID = 'gi|6273284|gb|AF191658.1|AF191', Name='<unknown name>',
 Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
 ID = 'gi|6273287|gb|AF191661.1|AF191', Name='<unknown name>',
 Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
 ...
 ID = 'gi|6273291|gb|AF191665.1|AF191', Name='<unknown name>',
 Seq='TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
Testing reading clustal format file Clustalw/opuntia.aln as an alignment
 TTTTTTT alignment column 0
 AAAAAAA alignment column 1
 TTTTTTT alignment column 2
 AAAAAAA alignment column 3
 CCCCCCC alignment column 4
 ||||||| ...
 AAAAAAA alignment column 155
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|6273291|gb|AF191665.1|AF191' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading clustal format file Clustalw/hedgehog.aln
 ID = 'gi|167877390|gb|EDS40773.1|', Name='<unknown name>',
 Seq='MFNLVSGTGGSSCCHRRNCFANRKKFFTMLLIFLLYMVSQ...-------', length=447
 ID = 'gi|167234445|ref|NP_001107837.', Name='<unknown name>',
 Seq='---------------------MRSASAAALLLAALLVVQA...-------', length=447
 ID = 'gi|74100009|gb|AAZ99217.1|', Name='<unknown name>',
 Seq='-------------MPQR----SLRHQLGMILVFFLLVTSH...D------', length=447
 ...
 ID = 'gi|56122354|gb|AAV74328.1|', Name='<unknown name>',
 Seq='----------------------LAADDQGRLLYSDFLTFL...GMAVKSS', length=447
Testing reading clustal format file Clustalw/hedgehog.aln as an alignment
 M---- alignment column 0
 F---- alignment column 1
 N---- alignment column 2
 L---- alignment column 3
 V---- alignment column 4
 ||||| ...
 ---SS alignment column 446
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|56122354|gb|AAV74328.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading clustal format file Clustalw/odd_consensus.aln
 ID = 'AT3G20900.1-CDS', Name='<unknown name>',
 Seq='----------------------------------------...AGAGTAG', length=687
 ID = 'AT3G20900.1-SEQ', Name='<unknown name>',
 Seq='ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAAC...AGAGTAG', length=687
Testing reading clustal format file Clustalw/odd_consensus.aln as an alignment
 -A alignment column 0
 -T alignment column 1
 -G alignment column 2
 -A alignment column 3
 -A alignment column 4
 || ...
 GG alignment column 686
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-CDS'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-CDS'), possibly due to truncation
Testing reading fasta format file Fasta/lupine.nu
 ID and Name='gi|5049839|gb|AI730987.1|AI730987',
 Seq='GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTC...GGTTTTT', length=655
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|5049839|gb|AI730987.1|AI730987' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/elderberry.nu
 ID and Name='gi|4218935|gb|AF074388.1|AF074388',
 Seq='ATGAAGTTAAGCACTCTTCTCATCTTATCTTTTCCTTTCC...GTCGTTT', length=2050
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|4218935|gb|AF074388.1|AF074388' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/phlox.nu
 ID and Name='gi|5052071|gb|AF067555.1|AF067555',
 Seq='TCGAAACCTGCCTAGCAGAACGACCCGCGAACTTGTATTC...CACGACC', length=623
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|5052071|gb|AF067555.1|AF067555' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/centaurea.nu
 ID and Name='gi|4104054|gb|AH007193.1|SEG_CVIGS',
 Seq='CCTGTCACTTAACTTTTTGTTCATAAGGTATATATGGGGG...GTTAGAG', length=1002
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|4104054|gb|AH007193.1|SEG_CVIGS' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/wisteria.nu
 ID and Name='gi|5817701|gb|AF142731.1|AF142731',
 Seq='GCTCCATTTTTTACACATTTCTATGAACTAATTGGTTCAT...ATGATGA', length=2551
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|5817701|gb|AF142731.1|AF142731' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/sweetpea.nu
 ID and Name='gi|3176602|gb|U78617.1|LOU78617',
 Seq='CAGGCTGCGCGGTTTCTATTTATGAAGAACAAGGTCCGTA...GTTTGTT', length=309
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|3176602|gb|U78617.1|LOU78617' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/lavender.nu
 ID and Name='gi|5690369|gb|AF158246.1|AF158246',
 Seq='GGCTCTTAAGTCATGTCTAGGCAGGTGTGCACAAGTTTAG...GTAGGTG', length=550
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|5690369|gb|AF158246.1|AF158246' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/aster.pro
 ID and Name='gi|3298468|dbj|BAA31520.1|',
 Seq='GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLL...FIVGANI', length=107
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|3298468|dbj|BAA31520.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/loveliesbleeding.pro
 ID and Name='gi|2781234|pdb|1JLY|B',
 Seq='XAGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKIL...IELGQNN', length=304
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|2781234|pdb|1JLY|B' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/rose.pro
 ID and Name='gi|4959044|gb|AAD34209.1|AF069992_1',
 Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=600
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|4959044|gb|AAD34209.1|AF069992_1' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/rosemary.pro
 ID and Name='gi|671626|emb|CAA85685.1|',
 Seq='MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAF...FEFPAMD', length=473
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|671626|emb|CAA85685.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/f001
 ID and Name='gi|3318709|pdb|1A91|',
 Seq='MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAA...YVMFAVA', length=79
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|3318709|pdb|1A91|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Fasta/f002
 ID and Name='gi|1348912|gb|G26680|G26680',
 Seq='CGGACCAGACGGACACAGGGAGAAGCTAGTTTCTTTCATG...GGTTTNA', length=633
 ID and Name='gi|1348917|gb|G26685|G26685',
 Seq='CGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATC...NNNGAAA', length=413
 ID and Name='gi|1592936|gb|G29385|G29385',
 Seq='GATCAAATCTGCACTGTGTCTACATATAGGAAAGGTCCTG...NTTTTTT', length=471
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|1592936|gb|G29385|G29385' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading fasta format file Fasta/fa01
 ID and Name='AK1H_ECOLI/1-378',
 Seq='CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDP...INIVAIA', length=378
 ID and Name='AKH_HAEIN/1-382',
 Seq='-----------------VEDAVKATIDCRGEKLSIAMMKA...SALAQAN', length=382
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading fasta format file GenBank/NC_005816.fna
 ID and Name='gi|45478711|ref|NC_005816.1|',
 Seq='TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTG...ACCCCTG', length=9609
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|45478711|ref|NC_005816.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file GenBank/NC_005816.ffn
 ID and Name='ref|NC_005816.1|:87-1109',
 Seq='ATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGC...GGCGTGA', length=1023
 ID and Name='ref|NC_005816.1|:1106-1888',
 Seq='GTGATGATGGAACTGCAACATCAACGACTGATGGCGCTCG...TGAGTAA', length=783
 ID and Name='ref|NC_005816.1|:2925-3119',
 Seq='GTGAACAAACAACAACAAACTGCGCTGAATATGGCGCGAT...AACATAA', length=195
 ...
 ID and Name='ref|NC_005816.1|:c8360-8088',
 Seq='TTGGCTGATTTGAAAAAGCTACAGGTTTACGGACCTGAGT...CAAGTAA', length=273
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'ref|NC_005816.1|:c8360-8088' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading fasta format file GenBank/NC_005816.faa
 ID and Name='gi|45478712|ref|NP_995567.1|',
 Seq='MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQA...SFCRGVA', length=340
 ID and Name='gi|45478713|ref|NP_995568.1|',
 Seq='MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSY...IAEANPE', length=260
 ID and Name='gi|45478714|ref|NP_995569.1|',
 Seq='MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCER...AESETGT', length=64
 ...
 ID and Name='gi|45478721|ref|NP_995576.1|',
 Seq='MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGR...LNTLESK', length=90
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|45478721|ref|NP_995576.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading fasta format file GenBank/NC_000932.faa
 ID and Name='gi|7525080|ref|NP_051037.1|',
 Seq='MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTI...YGVKKPK', length=123
 ID and Name='gi|7525013|ref|NP_051039.1|',
 Seq='MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPT...EAPSTNG', length=353
 ID and Name='gi|126022795|ref|NP_051040.2|',
 Seq='MDKFQGYLEFDGARQQSFLYPLFFREYIYVLAYDHGLNRL...NDLVNHE', length=504
 ...
 ID and Name='gi|7525099|ref|NP_051123.1|',
 Seq='MAIHLYKTSTPSTRNGAVDSQVKSNPRNNLICGQHHCGKG...ILRRRSK', length=274
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|7525099|ref|NP_051123.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading tab format file GenBank/NC_005816.tsv
 ID and Name='gi|45478712|ref|NP_995567.1|',
 Seq='MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQA...SFCRGVA', length=340
 ID and Name='gi|45478713|ref|NP_995568.1|',
 Seq='MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSY...IAEANPE', length=260
 ID and Name='gi|45478714|ref|NP_995569.1|',
 Seq='MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCER...AESETGT', length=64
 ...
 ID and Name='gi|45478721|ref|NP_995576.1|',
 Seq='MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGR...LNTLESK', length=90
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|45478721|ref|NP_995576.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading fasta format file GFF/NC_001802.fna
 ID and Name='gi|9629357|ref|NC_001802.1|',
 Seq='GGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTC...GTGCTTC', length=9181
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|9629357|ref|NC_001802.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file GFF/NC_001802lc.fna
 ID and Name='gi|9629357|ref|nc_001802.1|',
 Seq='ggtctctctggttagaccagatctgagcctgggagctctc...gtgcttc', length=9181
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|9629357|ref|nc_001802.1|' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file GFF/multi.fna
 ID and Name='test1',
 Seq='ACGTCGCG', length=8
 ID and Name='test2',
 Seq='GGGGCCCC', length=8
 ID and Name='test3',
 Seq='AAACACAC', length=8
Testing reading fasta format file GFF/multi.fna as an alignment
 AGA alignment column 0
 CGA alignment column 1
 GGA alignment column 2
 TGC alignment column 3
 CCA alignment column 4
 ||| ...
 GCC alignment column 7
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Registry/seqs.fasta
 ID and Name='gi|1348916|gb|G26684|G26684',
 Seq='GATCCCTACCCTTNCCGTTGGTCTCTNTCGCTGACTCGAG...TTATTTC', length=285
 ID and Name='gi|129628|sp|P07175|PARA_AGRTU',
 Seq='MPVVVVASSKGGAGKSTTAVVLGTELAHKGVPVTMLDCDP...KLTEALR', length=222
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|129628|sp|P07175|PARA_AGRTU' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading nexus format file Nexus/test_Nexus_input.nex
 ID and Name='t1',
 Seq='A-C-G-Tc-gtgtgtgctct-t-t------ac-gtgtgtgctct-t-t', length=48
 ID and Name='t2 the name',
 Seq='A-C-GcTc-gtg-----tct-t-t----acac-gtg-----tct-t-t', length=48
 ID and Name='isn'that [a] strange name?',
 Seq='A-CcGcTc-gtgtgtgct--------acacac-gtgtgtgct------', length=48
 ...
 ID and Name='t9',
 Seq='cccccccc-cccccccccccNc-ccccccccc-cccccccccccNc-c', length=48
Testing reading nexus format file Nexus/test_Nexus_input.nex as an alignment
 AAAAAAAAc alignment column 0
 -----c?tc alignment column 1
 CCCCCCCCc alignment column 2
 --c-?a-tc alignment column 3
 GGGGGGGGc alignment column 4
 ||||||||| ...
 tt--?ag?c alignment column 47
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: one should be punished, for (that)!
 Checking can write/read as 'embl' format
 Failed: Cannot have spaces in EMBL accession, 'one should be punished, for (that)!'
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'one should be punished, for (that)!' is too long
 Checking can write/read as 'imgt' format
 Failed: Cannot have spaces in EMBL accession, 'one should be punished, for (that)!'
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp001
 ID = 'Q13454', Name='N33_HUMAN',
 Seq='MGARGAPSRRRQAGRRLRYLPTGSFPFLLLLLLLCIQLGG...YSDLDFE', length=348
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp002
 ID = 'P54101', Name='CSP_MOUSE',
 Seq='MADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYRKLAL...YHTDGFN', length=198
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp003
 ID = 'P42655', Name='143E_HUMAN',
 Seq='MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVE...DVEDENQ', length=255
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp004
 ID = 'P23082', Name='NDOA_PSEPU',
 Seq='TVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYAT...RVMIDLS', length=103
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp005
 ID = 'P24973', Name='NU3M_BALPH',
 Seq='MNLLLTLLTNTTLALLLVFIAFWLPQLNVYAEKTSPYECG...EGLEWAE', length=115
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp006
 ID = 'P39896', Name='TCMO_STRGA',
 Seq='MTPHTHVRGPGDILQLTMAFYGSRALISAVELDLFTLLAG...AIGRKPR', length=339
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp007
 ID = 'O95832', Name='CLD1_HUMAN',
 Seq='MANAGLQLLGFILAFLGWIGAIVSTALPQWRIYSYAGDNI...SSGKDYV', length=211
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp008
 ID = 'P01892', Name='1A02_HUMAN',
 Seq='MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPG...SLTACKV', length=365
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp009
 ID = 'O23729', Name='CHS3_BROFI',
 Seq='MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDY...VPIAGAE', length=394
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp010
 ID = 'Q13639', Name='5H4_HUMAN',
 Seq='MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLV...AAQPSDT', length=388
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp011
 ID = 'P16235', Name='LSHR_RAT',
 Seq='MGRRVPALRQLLVLAVLLLKPSQLQSRELSGSRCPEPCDC...PPRALTH', length=700
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp012
 ID and Name='Q9Y736',
 Seq='MQIFVKTLTGKTITLEVESSDTIDNVKTKIQDKEGIPPDQ...LRLRGGN', length=153
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736).
 Checking can write/read as 'seqxml' format
 Failed: ncbiTaxID should be of type string or int
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp013
 ID and Name='P82909',
 Seq='MGSKMASASRVVQVVKPHTPLIRFPDRRDNPKPNVSEALR...IQRGGPE', length=102
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp014
 ID = 'P12166', Name='PSBL_ORYSA',
 Seq='TQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN', length=37
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166).
 Checking can write/read as 'seqxml' format
 Failed: ncbiTaxID should be of type string or int
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp015
 ID = 'IPI00383150', Name='IPI00383150.2',
 Seq='MSFQAPRRLLELAGQSLLRDQALAISVLDELPRELFPRLF...FIGPTPC', length=457
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/sp016
 ID = 'P01100', Name='FOS_HUMAN',
 Seq='MMFSGFNADYEASSSRCSSASPAGDSLSYYHSPADSFSSM...SPTLLAL', length=380
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file Registry/EDD_RAT.dat
 ID = 'Q62671', Name='EDD_RAT',
 Seq='ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFL...TKNFGFV', length=920
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading uniprot-xml format file SwissProt/uni001
 ID = 'Q91G55', Name='043L_IIV6',
 Seq='MDLINNKLNIEIQKFCLDLEKKYNINYNNLIDLWFNKEST...CLNDIPI', length=116
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q91G55).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q91G55).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q91G55).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q91G55).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q91G55).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading uniprot-xml format file SwissProt/uni002
 ID = 'Q91G55', Name='043L_IIV6',
 Seq='MDLINNKLNIEIQKFCLDLEKKYNINYNNLIDLWFNKEST...CLNDIPI', length=116
 ID = 'O55717', Name='094L_IIV6',
 Seq='MSGGSLINSIAINTRIKKIKKSLLQNYTKEKTDMIKILYL...SSEHMTV', length=118
 ID = 'P0C9J6', Name='11011_ASFP4',
 Seq='MYFYKKYLHFFFVVSKFKFFLKMQVPFGCNMKGLGVLLGL...SLPTYYG', length=302
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P0C9J6).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P0C9J6).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P0C9J6).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P0C9J6).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P0C9J6).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading uniprot-xml format file SwissProt/Q13639.xml
 ID = 'Q13639', Name='5HT4R_HUMAN',
 Seq='MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLV...AAQPSDT', length=388
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/Q13639.txt
 ID = 'Q13639', Name='5HT4R_HUMAN',
 Seq='MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLV...AAQPSDT', length=388
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading uniprot-xml format file SwissProt/H2CNN8.xml
 ID = 'H2CNN8', Name='H2CNN8_9ARCH',
 Seq='FIVVVAVNSTLLTINAGDYIFYTDWAWTSFVVFSISQSTM...LNTWTYR', length=196
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/H2CNN8.txt
 ID = 'H2CNN8', Name='H2CNN8_9ARCH',
 Seq='FIVVVAVNSTLLTINAGDYIFYTDWAWTSFVVFSISQSTM...LNTWTYR', length=196
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=H2CNN8).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading uniprot-xml format file SwissProt/F2CXE6.xml
 ID = 'F2CXE6', Name='F2CXE6_HORVD',
 Seq='MTMAAAQGKLSPDAIDNEVISNGSAKDYLDPPPAPLVDAG...SNYDAAV', length=291
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading swiss format file SwissProt/F2CXE6.txt
 ID = 'F2CXE6', Name='F2CXE6_HORVD',
 Seq='MTMAAAQGKLSPDAIDNEVISNGSAKDYLDPPPAPLVDAG...SNYDAAV', length=291
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=F2CXE6).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/noref.gb
 ID = 'NM_006141.1', Name='NM_006141',
 Seq='GGCAAGATGGCGCCGGTGGGGGTGGAGAAGAAGCTGCTGC...AAAAAAA', length=1622
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/cor6_6.gb
 ID = 'X55053.1', Name='ATCOR66M',
 Seq='AACAAAACACACATCAAAAACGATTTTACAAGAAAAAAAT...AAAAAAA', length=513
 ID = 'X62281.1', Name='ATKIN2',
 Seq='ATTTGGCCTATAAATATAAACCCTTAAGCCCACATATCTT...AATTATA', length=880
 ID = 'M81224.1', Name='BNAKINI',
 Seq='AAAAAAACACAACAAAACTCAATAAATAAACAAATGGCAG...AAGCTTC', length=441
 ...
 ID = 'AF297471.1', Name='AF297471',
 Seq='ATGGCAGACAACAAGCAGAGCTTCCAAGCCGGTCAAGCCG...CAAGTAG', length=497
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading genbank format file GenBank/iro.gb
 ID = 'AL109817.1', Name='IRO125195',
 Seq='CACAGGCCCAGAGCCACTCCTGCCTACAGGTTCTGAGGGC...AAAAAAA', length=1326
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/pri1.gb
 ID = 'U05344.1', Name='HUGLUT1',
 Seq='GATCATGCATGCACTCCAGCCTGGGACAAGAGCGAAACTC...GTTTGCA', length=741
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/arab1.gb
 ID = 'AC007323.5', Name='AC007323',
 Seq='AAGCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTT...GAAGCTT', length=86436
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/protein_refseq.gb
 ID = 'NP_034640.1', Name='NP_034640',
 Seq='MNNRWILHAAFLLCFSTTALSINYKQLQLQERTNIRKCQE...LTRNFQN', length=182
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/protein_refseq2.gb
 ID = 'NP_034640.1', Name='NP_034640',
 Seq='MNNRWILHAAFLLCFSTTALSINYKQLQLQERTNIRKCQE...LTRNFQN', length=182
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/extra_keywords.gb
 ID = 'AL138972.1', Name='DMBR25B3',
 Seq='TCCAGGGGATTCACGCGCAATATGTTTCCCTCGCTCGTCT...TCGATTG', length=154329
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/one_of.gb
 ID = 'U18266.1', Name='HSTMPO1',
 Seq='GAATTCAGATAGAATGTAGACAAGAGGGATGGTGAGGAAA...CAAAGGC', length=2509
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/NT_019265.gb
 ID = 'NT_019265.6', Name='NT_019265',
 Seq='NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNN', length=1250660
 Checking can write/read as 'embl' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NT_019265.6).
Testing reading genbank format file GenBank/origin_line.gb
 ID = 'NC_002678.1', Name='NC_002678',
 Seq='TTAATTAACTGTCTTCGATTGCGTTTAATTGACGGTTTTC...TCAGCGC', length=180
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/blank_seq.gb
 ID = 'NP_001832.1', Name='NP_001832',
 Seq='MEECWVTEIANGSKDGLDSNPMKDYMILSGPQKTAVAVLC...DLDLSDC', length=360
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/dbsource_wrap.gb
 ID = 'P01485', Name='SCX3_BUTOC',
 Seq='VKDGYIVDDRNCTYFCGRNAYCNEECTKLKGESGYCQWAS...KGPGRCN', length=64
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/NC_005816.gb
 ID = 'NC_005816.1', Name='NC_005816',
 Seq='TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTG...ACCCCTG', length=9609
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/NC_000932.gb
 ID = 'NC_000932.1', Name='NC_000932',
 Seq='ATGGGCGAACGACGGGAATTGAACCCGCGATGGTGAATTC...GGGCATC', length=154478
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/pBAD30.gb
 ID and Name='pBAD30',
 Seq='GCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGAT...GCCCATG', length=4923
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/gbvrl1_start.seq
 ID = 'AB000048.1', Name='AB000048',
 Seq='ATGTCTGGCAACCAGTATACTGAGGAAGTTATGGAGGGAG...GGATTAA', length=2007
 ID = 'AB000049.1', Name='AB000049',
 Seq='ATGTCTGGCAACCAGTATACTGAGGAAGTTATGGAGGGAG...GGATTAA', length=2007
 ID = 'AB000050.1', Name='AB000050',
 Seq='ATGAGTGATGGAGCAGTTCAACCAGACGGTGGTCAACCTG...ATATTAA', length=1755
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading genbank format file GFF/NC_001422.gbk
 ID = 'NC_001422.1', Name='NC_001422',
 Seq='GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCG...ACCTGCA', length=5386
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/NP_416719.gbwithparts
 ID = 'NP_416719.1', Name='NP_416719',
 Seq='MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDG...LGLVYQF', length=367
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_416719.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_416719.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_416719.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_416719.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_416719.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading genbank format file GenBank/1MRR_A.gp
 ID and Name='1MRR_A',
 Seq='AYTTFSATKNDQLKEPMFFGQPVQVARYDQQKYDIFEKLI...DLSNFQL', length=375
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=1MRR_A).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=1MRR_A).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=1MRR_A).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=1MRR_A).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=1MRR_A).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/epo_prt_selection.embl
 ID = 'A00022.1', Name='A00022',
 Seq='CLARIIRYFYNAKA', length=14
 ID = 'A00028.1', Name='A00028',
 Seq='CIARIIRYFYNAKA', length=14
 ID = 'A00031.1', Name='A00031',
 Seq='RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRA...ERTCGGA', length=58
 ...
 ID = 'CQ797900.1', Name='CQ797900',
 Seq='MAIGTLEATTLIRGRAMTTVLPSPELIASFVDIVGPGNAL...LREDRGE', length=496
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading embl format file EMBL/patents.embl
 ID and Name='NRP00000001',
 Seq='XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXX', length=358
 ID and Name='NRP00000002',
 Seq='XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXX', length=65
 ID and Name='NRP00210944',
 Seq='XXXXXXXXXXXXXXXXXXXXXXXXX', length=25
 ID and Name='NRP00210945',
 Seq='XXXXXXXXXXXXXXXXXXXXXXXXX', length=25
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NRP00210945).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NRP00210945).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NRP00210945).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NRP00210945).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NRP00210945).
 Checking can write/read as 'seqxml' format
 Failed: Sequence type is UnknownSeq but SeqXML requires sequence
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading embl format file EMBL/TRBG361.embl
 ID = 'X56734.1', Name='X56734',
 Seq='AAACAAACCAAATATGGATTTTATTGTAGCCATATTTGCT...AAAAAAA', length=1859
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/DD231055_edited.embl
 ID = 'DD231055.1', Name='DD231055',
 Seq='GCCGAGCTGACCCAGTCTCCATCCTCCCTGTCTGCATCTG...TATGAGA', length=315
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/DD231055_edited2.embl
 ID = 'DD231055.1', Name='DD231055',
 Seq='GCCGAGCTGACCCAGTCTCCATCCTCCCTGTCTGCATCTG...TATGAGA', length=315
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/SC10H5.embl
 ID = 'AL031232', Name='SC10H5',
 Seq='GATCAGTAGACCCAGCGACAGCAGGGCGGGGCCCAGCAGG...CGAGCAT', length=4870
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/U87107.embl
 ID = 'U87107.1', Name='U87107',
 Seq='CAATTACTGCAATGCCCTCGTAATTAAGTGAATTTACAAT...CATCACC', length=8840
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/AAA03323.embl
 ID = 'AAA03323.1', Name='AAA03323',
 Seq='ATGAAGCTTTTAGTGCGCCTAGCACCGATCCTGCTGCTAG...GGTGTGA', length=1545
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/AE017046.embl
 ID = 'AE017046.1', Name='AE017046',
 Seq='TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTG...ACCCCTG', length=9609
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/Human_contigs.embl
 ID = 'AJ229040.1', Name='AJ229040',
 Seq='NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNN', length=958952
 ID = 'AL954800.2', Name='AL954800',
 Seq='NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNN', length=87191216
 Checking can write/read as 'embl' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL954800.2).
Testing reading embl format file EMBL/location_wrap.embl
 ID = 'Test', Name='Tester',
 Seq='CGACTTTCCACTGCCCTCTACGCCCGCGCAATGGGTCGTA...CTACGTT', length=120
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Test).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Test).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Test).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Test).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Test).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/A04195.imgt
 ID and Name='A04195',
 Seq='GATTGATCAATGCAGGCTGTTATGACTCAGGAATCTGCAC...CACATCA', length=51
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading imgt format file EMBL/A04195.imgt
 ID and Name='A04195',
 Seq='GATTGATCAATGCAGGCTGTTATGACTCAGGAATCTGCAC...CACATCA', length=51
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading stockholm format file Stockholm/simple.sth
 ID and Name='AP001509.1',
 Seq='UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAU...UUAAUGU', length=104
 ID and Name='AE007476.1',
 Seq='AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-U...GUGAGAU', length=104
Testing reading stockholm format file Stockholm/simple.sth as an alignment
 UA alignment column 0
 UA alignment column 1
 AA alignment column 2
 AA alignment column 3
 UU alignment column 4
 || ...
 UU alignment column 103
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading stockholm format file Stockholm/funny.sth
 ID = 'O83071/192-246', Name='O83071',
 Seq='MTCRAQLIAVPRASSLAE--AIACAQKM----RVSRVPVYERS', length=43
 ID = 'O83071/259-312', Name='O83071',
 Seq='MQHVSAPVFVFECTRLAY--VQHKLRAH----SRAVAIVLDEY', length=43
 ID = 'O31698/18-71', Name='O31698',
 Seq='MIEADKVAHVQVGNNLEH--ALLVLTKT----GYTAIPVLDPS', length=43
 ...
 ID and Name='363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00',
 Seq='EVMLTDIPRLHINDPIMK--GFGMVINN------GFVCVENDE', length=43
Testing reading stockholm format file Stockholm/funny.sth as an alignment
 MMMEEE alignment column 0
 TQIVVV alignment column 1
 CHEMMM alignment column 2
 RVALLL alignment column 3
 ASDTTT alignment column 4
 |||||| ...
 SYSEEE alignment column 42
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier '363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/reference_dna.phy
 ID and Name='Archaeopt',
 Seq='CGATGCTTACCGC', length=13
 ID and Name='Hesperorni',
 Seq='CGTTACTCGTTGT', length=13
 ID and Name='Baluchithe',
 Seq='TAATGTTAATTGT', length=13
 ...
 ID and Name='B.subtilis',
 Seq='GGCAGCCAATCAC', length=13
Testing reading phylip format file Phylip/reference_dna.phy as an alignment
 CCTTCG alignment column 0
 GGAAAG alignment column 1
 ATAAAC alignment column 2
 TTTTAA alignment column 3
 GAGGAG alignment column 4
 |||||| ...
 CTTTTC alignment column 12
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: B. virgini
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/reference_dna2.phy
 ID and Name='Archaeopt',
 Seq='CGATGCTTACCGCCGATGCTTACCGCCGATGCTTACCGC', length=39
 ID and Name='Hesperorni',
 Seq='CGTTACTCGTTGTCGTTACTCGTTGTCGTTACTCGTTGT', length=39
 ID and Name='Baluchithe',
 Seq='TAATGTTAATTGTTAATGTTAATTGTTAATGTTAATTGT', length=39
 ...
 ID and Name='B.subtilis',
 Seq='GGCAGCCAATCACGGCAGCCAATCACGGCAGCCAATCAC', length=39
Testing reading phylip format file Phylip/reference_dna2.phy as an alignment
 CCTTCG alignment column 0
 GGAAAG alignment column 1
 ATAAAC alignment column 2
 TTTTAA alignment column 3
 GAGGAG alignment column 4
 |||||| ...
 CTTTTC alignment column 38
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: B. virgini
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/hennigian.phy
 ID and Name='A',
 Seq='CACACACAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40
 ID and Name='B',
 Seq='CACACAACAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40
 ID and Name='C',
 Seq='CACAACAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40
 ...
 ID and Name='J',
 Seq='ACAAAAAAAAACAAAAACACAAAAAAAAAAAAAAAAAAAA', length=40
Testing reading phylip format file Phylip/hennigian.phy as an alignment
 CCCCCAAAAA alignment column 0
 AAAAACCCCC alignment column 1
 CCCAAAAAAA alignment column 2
 AAACCAAAAA alignment column 3
 CCAAAAAAAA alignment column 4
 |||||||||| ...
 AAAAAAAAAA alignment column 39
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/horses.phy
 ID and Name='Mesohippus',
 Seq='AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA', length=40
 ID and Name='Hypohippus',
 Seq='AAACCCCCCCAAAAAAAAACAAAAAAAAAAAAAAAAAAAA', length=40
 ID and Name='Archaeohip',
 Seq='CAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAA', length=40
 ...
 ID and Name='Pliohippus',
 Seq='CCCACCCCCCCCCACACCCCAAAAAAAAAAAAAAAAAAAA', length=40
Testing reading phylip format file Phylip/horses.phy as an alignment
 AACCCCCCCC alignment column 0
 AAAACCCCCC alignment column 1
 AAAAAAAAAC alignment column 2
 ACAAAAAAAA alignment column 3
 ACACCCCCCC alignment column 4
 |||||||||| ...
 AAAAAAAAAA alignment column 39
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: M. secundu
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/random.phy
 ID and Name='A',
 Seq='CACACAACCAAACAAACCACAAAAAAAAAAAAAAAAAAAA', length=40
 ID and Name='B',
 Seq='AAACCACACACACAAACCCAAAAAAAAAAAAAAAAAAAAA', length=40
 ID and Name='C',
 Seq='ACAAAACCAAACCACCCACAAAAAAAAAAAAAAAAAAAAA', length=40
 ...
 ID and Name='J',
 Seq='CCAAAAACACCCAACCCAACAAAAAAAAAAAAAAAAAAAA', length=40
Testing reading phylip format file Phylip/random.phy as an alignment
 CAAAACAAAC alignment column 0
 AACAACCACC alignment column 1
 CAAAACAAAA alignment column 2
 ACAACACACA alignment column 3
 CCAAAACCAA alignment column 4
 |||||||||| ...
 AAAAAAAAAA alignment column 39
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/interlaced.phy
 ID and Name='CYS1_DICDI',
 Seq='-----MKVILLFVLAVFTVFVSS---------------RG...STSII--', length=384
 ID and Name='ALEU_HORVU',
 Seq='MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRA...SYPVVAA', length=384
 ID and Name='CATH_HUMAN',
 Seq='------MWATLPLLCAGAWLLGV--------PVCGAAELS...SYPIPLV', length=384
Testing reading phylip format file Phylip/interlaced.phy as an alignment
 -M- alignment column 0
 -A- alignment column 1
 -H- alignment column 2
 -A- alignment column 3
 -R- alignment column 4
 ||| ...
 -AV alignment column 383
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phylip format file Phylip/interlaced2.phy
 ID and Name='IXI_234',
 Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131
 ID and Name='IXI_235',
 Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131
 ID and Name='IXI_236',
 Seq='TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCC...AGDRSHE', length=131
 ID and Name='IXI_237',
 Seq='TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----C...AGDRSHE', length=131
Testing reading phylip format file Phylip/interlaced2.phy as an alignment
 TTTT alignment column 0
 SSSS alignment column 1
 PPPP alignment column 2
 AAAA alignment column 3
 SSSS alignment column 4
 |||| ...
 EEEE alignment column 130
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading emboss format file Emboss/alignret.txt
 ID = 'IXI_234', Name='<unknown name>',
 Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131
 ID = 'IXI_235', Name='<unknown name>',
 Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131
 ID = 'IXI_236', Name='<unknown name>',
 Seq='TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCC...AGDRSHE', length=131
 ID = 'IXI_237', Name='<unknown name>',
 Seq='TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----C...AGDRSHE', length=131
Testing reading emboss format file Emboss/alignret.txt as an alignment
 TTTT alignment column 0
 SSSS alignment column 1
 PPPP alignment column 2
 AAAA alignment column 3
 SSSS alignment column 4
 |||| ...
 EEEE alignment column 130
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading emboss format file Emboss/needle.txt
 ID = 'ref_rec', Name='<unknown name>',
 Seq='KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQAL...-------', length=124
 ID = 'gi|94968718|receiver', Name='<unknown name>',
 Seq='-VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAV...RVANGET', length=124
 ID = 'ref_rec', Name='<unknown name>',
 Seq='KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVT...-------', length=119
 ...
 ID = 'gi|94970041|receiver', Name='<unknown name>',
 Seq='TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVR...AVLQKRQ', length=125
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'gi|94970041|receiver' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading emboss format file Emboss/water.txt
 ID = 'IXI_234', Name='<unknown name>',
 Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131
 ID = 'IXI_235', Name='<unknown name>',
 Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131
Testing reading emboss format file Emboss/water.txt as an alignment
 TT alignment column 0
 SS alignment column 1
 PP alignment column 2
 AA alignment column 3
 SS alignment column 4
 || ...
 EE alignment column 130
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading phd format file Phd/phd1
 ID and Name='34_222_(80-A03-19).b.ab1',
 Seq='ctccgtcggaacatcatcggatcctatcacagagtttttg...aagcgtg', length=876
 ID and Name='425_103_(81-A03-19).g.ab1',
 Seq='cgggatcccacctgatccgaggtcaacctgaaaaaatatg...agccaag', length=862
 ID and Name='425_7_(71-A03-19).b.ab1',
 Seq='acataaatcaaattactnaccaacacacaaaccngtctcg...tgctttn', length=1280
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier '425_7_(71-A03-19).b.ab1' is too long
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading phd format file Phd/phd2
 ID and Name='ML4924R',
 Seq='actttggtcgcctgcaggtaccggtccgngattcccgggt...ggtgaga', length=180
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading phd format file Phd/phd_solexa
 ID and Name='HWI-EAS94_4_1_1_537_446',
 Seq='gccaatcaggtttctctgcaagcccctttagcagctgagc', length=40
 ID and Name='HWI-EAS94_4_1_1_602_99',
 Seq='gccatggcacatatatgaaggtcagaggacaacttgctgt', length=40
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'HWI-EAS94_' (originally 'HWI-EAS94_4_1_1_537_446'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'HWI-EAS94_4_1_1_602_99' is too long
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'HWI-EAS94_' (originally 'HWI-EAS94_4_1_1_537_446'), possibly due to truncation
Testing reading phd format file Phd/phd_454
 ID and Name='EBE03TV04IHLTF.77-243',
 Seq='ggggatgaaagggatctcggtggtaggtga', length=30
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'EBE03TV04IHLTF.77-243' is too long
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading ace format file Ace/contig1.ace
 ID and Name='Contig1',
 Seq='aatacgGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAAC...CTAGtac', length=856
 ID and Name='Contig2',
 Seq='cacggatgatagcttcgcgacactagcttttcagctaacc...cttgtag', length=3296
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading ace format file Ace/consed_sample.ace
 ID and Name='Contig1',
 Seq='agccccgggccgtggggttccttgagcactcccaaagttc...gggtttg', length=1475
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading ace format file Ace/seq.cap.ace
 ID and Name='Contig1',
 Seq='AGTTTTAGTTTTCCTCTGAAGCAAGCACACCTTCCCTTTC...TCACATT', length=1222
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading ig format file IntelliGenetics/TAT_mase_nuc.txt
 ID and Name='A_U455',
 Seq='ATGGAGCCAGTAGATCCTAACCTAGAGCCCTGGAAACACC...ATTCGCT', length=303
 ID and Name='B_HXB2R',
 Seq='ATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATC...CGATTAG', length=306
 ID and Name='C_UG268A',
 Seq='%CAGGAAGTCAGCCTAAAACTCCTTGTACTAAGTGTTTTG...AGATTAA', length=267
 ...
 ID and Name='SYK_SYK',
 Seq='ATGTCCTCAACGGACCAGATATGCCAGACACAGAGGGTAC...GAATCTT', length=330
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt
 ID and Name='most-likely',
 Seq='MEN--RW-QVMIVWQVDRMRIRTWKSLVKHHMYRSKKA-K...-----GH', length=298
 ID and Name='U455',
 Seq='MEN--RW-QVMIVWQVDRMKIRTWNSLVKHHMYVSKKA-Q...-----RH', length=298
 ID and Name='HXB2R',
 Seq='MEN--RW-QVMIVWQVDRMRIRTWKSLVKHHMYVSGKA-R...-----GH', length=298
 ...
 ID and Name='SYK',
 Seq='MEK--EW-IVVPTWRMTPRQIDRLQHIIKTHKYKSKELEK...-------', length=298
Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt as an alignment
 MMMMMMMMMMMMMMMM alignment column 0
 EEEEEEETEEEENEEE alignment column 1
 NNNNNNNAEEEEQRKK alignment column 2
 --------DEEEEE-- alignment column 3
 --------KKKKKK-- alignment column 4
 |||||||||||||||| ...
 HHHHHHH-AAAAL-R- alignment column 297
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading ig format file IntelliGenetics/vpu_nucaligned.txt
 ID and Name='VPU_CONSENSUS',
 Seq='ATGc?tcattt?ga??t?ttagcaaTaa?agcattaatag...?gA?ctg', length=294
 ID and Name='A_U455',
 Seq='ATGACACCTTTGGAAATCTGGGCAATAACAGGGCTGATAG...-AATTTG', length=294
 ID and Name='B_SF2',
 Seq='ATGCAATCTTTACAAATATTAGCAATAGTATCATTAGTAG...-GATCTG', length=294
 ...
 ID and Name='CPZANT',
 Seq='ATGACTAATATATTTGAGTATGCTTTT-------------...-GACGAA', length=294
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT).
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading pir format file NBRF/B_nuc.pir
 ID and Name='HLA:HLA00132',
 Seq='ATGCTGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCT...AGCTTGA', length=1089
 ID and Name='HLA:HLA00133',
 Seq='ATGCTGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCT...AAGAGTT', length=1009
 ID and Name='HLA:HLA00134',
 Seq='GCTCCCACTCCATGAGGTATTTCTACACCTCCGTGTCCCG...CGCGCTG', length=546
 ...
 ID and Name='HLA:HLA01135',
 Seq='ATGCGGGTCACGGCGCCCCGAACCCTCCTCCTGCTGCTCT...CGCGCGG', length=619
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading pir format file NBRF/Cw_prot.pir
 ID and Name='HLA:HLA00401',
 Seq='MRVMAPRTLILLLSGALALTETWACSHSMKYFFTSVSRPG...SLIACKA', length=366
 ID and Name='HLA:HLA00402',
 Seq='MRVMAPRTLILLLSGALALTETWACSHSMKYFFTSVSRPG...SLIACKA', length=366
 ID and Name='HLA:HLA01075',
 Seq='MRVMAPRTLILLLSGALALTETWACSHSMKYFFTSVSRPG...SLIACKA', length=366
 ...
 ID and Name='HLA:HLA00484',
 Seq='MRVMAPRALLLLLSGGLALTETWACSHSMRYFDTAVSRPG...SLIACKA', length=366
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading pir format file NBRF/DMA_nuc.pir
 ID and Name='HLA:HLA00485',
 Seq='ATGGGTCATGAACAGAACCAAGGAGCTGCGCTGCTACAGA...TGACTGA', length=786
 ID and Name='HLA:HLA00486',
 Seq='CTCCTACTCCAATGTGGCCAGATGACCTGCAAAACCACAC...TATTGGG', length=564
 ID and Name='HLA:HLA00487',
 Seq='GGGTTTCCTATCGCTGAAGTGTTCACGCTGAAGCCCCTGG...CTATTGG', length=279
 ID and Name='HLA:HLA00488',
 Seq='GGGTTTCCTATCGCTGAAGTGTTCACGCTGAAGCCCCTGG...CTATTGG', length=279
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading pir format file NBRF/DMB_prot.pir
 ID and Name='HLA:HLA00489',
 Seq='MITFLPLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDF...SEGWHIS', length=263
 ID and Name='HLA:HLA00490',
 Seq='PPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNG...EPILRDW', length=94
 ID and Name='HLA:HLA00491',
 Seq='PPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNG...EPILRDW', length=94
 ...
 ID and Name='HLA:HLA01083',
 Seq='GFVAHVESTCLLDDAGTPKDFTYCIFFNKDLLTCWDPEEN...EPILRDW', length=188
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083).
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading pir format file NBRF/clustalw.pir
 ID and Name='804Angiostrongylus_cantonensis',
 Seq='----------------------------------------...-------', length=2527
 ID and Name='815Parelaphostrongylus_odocoil',
 Seq='----------------------------------------...-------', length=2527
Testing reading pir format file NBRF/clustalw.pir as an alignment
 -- alignment column 0
 -- alignment column 1
 -- alignment column 2
 -- alignment column 3
 -- alignment column 4
 || ...
 -- alignment column 2526
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier '815Parelaphostrongylus_odocoil' is too long
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading fasta format file Quality/example.fasta
 ID and Name='EAS54_6_R1_2_1_413_324',
 Seq='CCCTTCTTGTCTTCAGCGTTTCTCC', length=25
 ID and Name='EAS54_6_R1_2_1_540_792',
 Seq='TTGGCAGGCCAAGGCCGATGGATCA', length=25
 ID and Name='EAS54_6_R1_2_1_443_348',
 Seq='GTTGCTTCTGGCGTGGGTGGGGGGG', length=25
Testing reading fasta format file Quality/example.fasta as an alignment
 CTG alignment column 0
 CTT alignment column 1
 CGT alignment column 2
 TGG alignment column 3
 TCC alignment column 4
 ||| ...
 CAG alignment column 24
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348).
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Testing reading qual format file Quality/example.qual
 ID and Name='EAS54_6_R1_2_1_413_324',
 Seq='?????????????????????????', length=25
 ID and Name='EAS54_6_R1_2_1_540_792',
 Seq='?????????????????????????', length=25
 ID and Name='EAS54_6_R1_2_1_443_348',
 Seq='?????????????????????????', length=25
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Sequence type is UnknownSeq but SeqXML requires sequence
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Testing reading fastq format file Quality/example.fastq
 ID and Name='EAS54_6_R1_2_1_413_324',
 Seq='CCCTTCTTGTCTTCAGCGTTTCTCC', length=25
 ID and Name='EAS54_6_R1_2_1_540_792',
 Seq='TTGGCAGGCCAAGGCCGATGGATCA', length=25
 ID and Name='EAS54_6_R1_2_1_443_348',
 Seq='GTTGCTTCTGGCGTGGGTGGGGGGG', length=25
Testing reading fastq format file Quality/example.fastq as an alignment
 CTG alignment column 0
 CTT alignment column 1
 CGT alignment column 2
 TGG alignment column 3
 TCC alignment column 4
 ||| ...
 CAG alignment column 24
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Testing reading fastq format file Quality/example_dos.fastq
 ID and Name='EAS54_6_R1_2_1_413_324',
 Seq='CCCTTCTTGTCTTCAGCGTTTCTCC', length=25
 ID and Name='EAS54_6_R1_2_1_540_792',
 Seq='TTGGCAGGCCAAGGCCGATGGATCA', length=25
 ID and Name='EAS54_6_R1_2_1_443_348',
 Seq='GTTGCTTCTGGCGTGGGTGGGGGGG', length=25
Testing reading fastq format file Quality/example_dos.fastq as an alignment
 CTG alignment column 0
 CTT alignment column 1
 CGT alignment column 2
 TGG alignment column 3
 TCC alignment column 4
 ||| ...
 CAG alignment column 24
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Testing reading fastq format file Quality/tricky.fastq
 ID and Name='071113_EAS56_0053:1:1:998:236',
 Seq='TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA', length=36
 ID and Name='071113_EAS56_0053:1:1:182:712',
 Seq='ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG', length=36
 ID and Name='071113_EAS56_0053:1:1:153:10',
 Seq='TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT', length=36
 ID and Name='071113_EAS56_0053:1:3:990:501',
 Seq='TGGGAGGTTTTATGTGGAAAGCAGCAATGTACAAGA', length=36
Testing reading fastq format file Quality/tricky.fastq as an alignment
 TATT alignment column 0
 TCGG alignment column 1
 TCTG alignment column 2
 CCTG alignment column 3
 TACA alignment column 4
 |||| ...
 AGTA alignment column 35
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name '071113_EAS' (originally '071113_EAS56_0053:1:1:153:10'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier '071113_EAS56_0053:1:3:990:501' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name '071113_EAS' (originally '071113_EAS56_0053:1:1:153:10'), possibly due to truncation
Testing reading fastq format file Quality/sanger_faked.fastq
 ID and Name='Test',
 Seq='ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN', length=41
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fastq format file Quality/sanger_93.fastq
 ID and Name='Test',
 Seq='ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTG...GACTGAN', length=94
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fastq-illumina format file Quality/illumina_faked.fastq
 ID and Name='Test',
 Seq='ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN', length=41
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Need a Nucleotide or Protein alphabet
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fastq-solexa format file Quality/solexa_faked.fastq
 ID and Name='slxa_0001_1_0001_01',
 Seq='ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN', length=46
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'slxa_0001_1_0001_01' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
Testing reading fastq-solexa format file Quality/solexa_example.fastq
 ID and Name='SLXA-B3_649_FC8437_R1_1_1_610_79',
 Seq='GATGTGCAATACCTTTGTAGAGGAA', length=25
 ID and Name='SLXA-B3_649_FC8437_R1_1_1_397_389',
 Seq='GGTTTGAGAAAGAGAAATGAGATAA', length=25
 ID and Name='SLXA-B3_649_FC8437_R1_1_1_850_123',
 Seq='GAGGGTGTTGATCATGATGATGGCG', length=25
 ...
 ID and Name='SLXA-B3_649_FC8437_R1_1_1_183_714',
 Seq='GTATTATTTAATGGCATACACTCAA', length=25
Testing reading fastq-solexa format file Quality/solexa_example.fastq as an alignment
 GGGGG alignment column 0
 AGAGT alignment column 1
 TTGAA alignment column 2
 GTGAT alignment column 3
 TTGAT alignment column 4
 ||||| ...
 AAGGA alignment column 24
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'SLXA-B3_64' (originally 'SLXA-B3_649_FC8437_R1_1_1_362_549'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'SLXA-B3_649_FC8437_R1_1_1_183_714' is too long
 Checking can write/read as 'imgt' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'SLXA-B3_64' (originally 'SLXA-B3_649_FC8437_R1_1_1_362_549'), possibly due to truncation
Testing reading seqxml format file SeqXML/dna_example.xml
 ID = 'ENSMUSG00000076441', Name='<unknown name>',
 Seq='CTTTGATTCACCATTTACTGGGAGCCCACGGCGATCTGGG...TCCCTGA', length=2460
 ID = 'fake1', Name='<unknown name>',
 Seq='ACGTMRWSYKVHDBXN.-', length=18
 ID = 'fake2', Name='<unknown name>',
 Seq='AAGGCGTTAAACCC', length=14
 ID = 'minimal', Name='<unknown name>',
 Seq='G', length=1
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=minimal).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=minimal).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=minimal).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'ENSMUSG00000076441' is too long
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=minimal).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=minimal).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading seqxml format file SeqXML/rna_example.xml
 ID = 'gga-let-7a-1', Name='<unknown name>',
 Seq='UGCACUGUGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGG...CCUAAAG', length=90
 ID = 'fake1', Name='<unknown name>',
 Seq='ACGUMRWSYKVHDBXN.-', length=18
 ID = 'fake2', Name='<unknown name>',
 Seq='GGAGAU', length=6
 ...
 ID = 'empty description', Name='<unknown name>',
 Seq='UGUGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCAUACCCGCAAC', length=48
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Failed: Cannot have spaces in EMBL accession, 'empty description'
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=empty description).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=empty description).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=empty description).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'empty description' is too long
 Checking can write/read as 'imgt' format
 Failed: Cannot have spaces in EMBL accession, 'empty description'
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=empty description).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=empty description).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading seqxml format file SeqXML/protein_example.xml
 ID = 'ENSMUSP00000099904', Name='<unknown name>',
 Seq='MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQ...QSKVTAK', length=412
 ID = 'fake1', Name='<unknown name>',
 Seq='ABCDEFGHIJKLMNOPQRSTUVWXYZ.-*', length=29
 ID = 'fake2', Name='<unknown name>',
 Seq='GAKKVFIEDVSKEFVEEFIWPAVQSSALYE', length=30
 ...
 ID = 'UniprotProtein', Name='<unknown name>',
 Seq='PPPWAKKVFIEDVIIAGSKEFVEEFIWPAVQSE', length=33
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'stockholm' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-relaxed' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=UniprotProtein).
 Checking can write/read as 'fastq-illumina' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=UniprotProtein).
 Checking can write/read as 'fastq-solexa' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=UniprotProtein).
 Checking can write/read as 'genbank' format
 Failed: Locus identifier 'ENSMUSP00000099904' is too long
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=UniprotProtein).
 Checking can write/read as 'qual' format
 Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=UniprotProtein).
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Failed: Sequences must all be the same length
 Checking can write/read as 'phylip-sequential' format
 Failed: Sequences must all be the same length
Testing reading abi format file Abi/310.ab1
 ID = 'D11F', Name='310',
 Seq='TGATNTTNACNNTTTTGAANCANTGAGTTAATAGCAATNC...NNNNNNG', length=868
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading abi format file Abi/3100.ab1
 ID = '16S_S2_1387R', Name='3100',
 Seq='CAAGATTGCATTCATGATCTACGATTACTAGCGATTCCAG...CCTTTTA', length=795
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Testing reading abi format file Abi/3730.ab1
 ID = '226032_C-ME-18_pCAGseqF', Name='3730',
 Seq='GGGCGAGCKYYAYATTTTGGCAAGAATTGAGCTCTATGGC...ACCTTTC', length=1165
 Checking can write/read as 'fasta' format
 Checking can write/read as 'clustal' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'embl' format
 Checking can write/read as 'fastq' format
 Checking can write/read as 'fastq-illumina' format
 Checking can write/read as 'fastq-solexa' format
 Checking can write/read as 'genbank' format
 Checking can write/read as 'imgt' format
 Checking can write/read as 'phd' format
 Checking can write/read as 'qual' format
 Checking can write/read as 'seqxml' format
 Checking can write/read as 'sff' format
 Failed: Missing SFF flow information
 Checking can write/read as 'tab' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip-sequential' format
Finished tested reading files
