# Copyright 2014 by Saket Choudhary.  Based on test_Clustalw_tool.py by Peter
# Cock .
#
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

# Last Checked with samtools [0.1.18 (r982:295)]

"""Tests for samtools tool."""

from Bio import MissingExternalDependencyError
import sys
import os
import unittest
import warnings


from Bio import BiopythonDeprecationWarning

with warnings.catch_warnings():
    warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
    from Bio.Application import ApplicationError
    from Bio.Sequencing.Applications import SamtoolsViewCommandline
    from Bio.Sequencing.Applications import SamtoolsCalmdCommandline
    from Bio.Sequencing.Applications import SamtoolsCatCommandline
    from Bio.Sequencing.Applications import SamtoolsFaidxCommandline
    from Bio.Sequencing.Applications import SamtoolsIdxstatsCommandline
    from Bio.Sequencing.Applications import SamtoolsIndexCommandline
    from Bio.Sequencing.Applications import SamtoolsMergeCommandline
    from Bio.Sequencing.Applications import SamtoolsMpileupCommandline
    from Bio.Sequencing.Applications import SamtoolsVersion1xSortCommandline
    from Bio.Sequencing.Applications import SamtoolsSortCommandline

# TODO from Bio.Sequencing.Applications import SamtoolsPhaseCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsReheaderCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsRmdupCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsTargetcutCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsFixmateCommandline
#################################################################
SamtoolsVersion0xSortCommandline = SamtoolsSortCommandline
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"

samtools_exe = None
if sys.platform == "win32":
    # TODO - Check the path?
    try:
        # This can vary depending on the Windows language.
        prog_files = os.environ["PROGRAMFILES"]
    except KeyError:
        prog_files = r"C:\Program Files"
    # By default tries C:\Program Files\samtools\samtools.exe
    # or  C:\Program Files\samtools.exe was chosen
    likely_dirs = ["samtools", ""]
    likely_exes = ["samtools.exe"]
    for folder in likely_dirs:
        if os.path.isdir(os.path.join(prog_files, folder)):
            for filename in likely_exes:
                if os.path.isfile(os.path.join(prog_files, folder, filename)):
                    samtools_exe = os.path.join(prog_files, folder, filename)
                    break
            if samtools_exe:
                break
else:
    from subprocess import getoutput

    output = getoutput("samtools")

    # Since "not found" may be in another language, try and be sure this is
    # really the samtools tool's output
    if (
        "not found" not in output
        and "samtools (Tools for alignments in the SAM format)" in output
    ):
        samtools_exe = "samtools"

if not samtools_exe:
    raise MissingExternalDependencyError(
        "Install samtools and correctly set the file path to "
        "the program if you want to use it from Biopython"
    )


class SamtoolsTestCase(unittest.TestCase):
    """Class for implementing Samtools test cases."""

    def setUp(self):
        self.files_to_clean = set()
        self.samfile1 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "sam1.sam"
        )
        self.reference = os.path.join(
            os.path.dirname(os.path.abspath(__file__)),
            "BWA",
            "human_g1k_v37_truncated.fasta",
        )
        self.referenceindexfile = os.path.join(
            os.path.dirname(os.path.abspath(__file__)),
            "BWA",
            "human_g1k_v37_truncated.fasta.fai",
        )
        self.samfile2 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "sam2.sam"
        )
        self.bamfile1 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam1.bam"
        )
        self.bamfile2 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam2.bam"
        )
        self.outsamfile = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "out.sam"
        )
        self.outbamfile = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "out.bam"
        )
        self.bamindexfile1 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam1.bam.bai"
        )
        self.sortedbamfile1 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam1_sorted.bam"
        )
        self.sortedbamfile2 = os.path.join(
            os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam2_sorted.bam"
        )
        self.files_to_clean = [
            self.referenceindexfile,
            self.bamindexfile1,
            self.outbamfile,
        ]

    def tearDown(self):
        for filename in self.files_to_clean:
            if os.path.isfile(filename):
                os.remove(filename)

    def test_view(self):
        """Test for samtools view."""
        cmdline = SamtoolsViewCommandline(samtools_exe)
        cmdline.set_parameter("input_file", self.bamfile1)
        stdout_bam, stderr_bam = cmdline()
        self.assertTrue(
            stderr_bam.startswith(""),
            f"SAM file viewing failed: \n{cmdline}\nStdout:{stdout_bam}",
        )
        cmdline.set_parameter("input_file", self.samfile1)
        cmdline.set_parameter("S", True)
        stdout_sam, stderr_sam = cmdline()
        self.assertTrue(
            stdout_sam.startswith("HWI-1KL120:88:D0LRBACXX:1:1101:1780:2146"),
            f"SAM file  viewing failed:\n{cmdline}\nStderr:{stderr_sam}",
        )

    def create_fasta_index(self):
        """Create index for reference fasta sequence."""
        cmdline = SamtoolsFaidxCommandline(samtools_exe)
        cmdline.set_parameter("reference", self.reference)
        stdout, stderr = cmdline()

    def create_bam_index(self, input_bam):
        """Create index of an input bam file."""
        cmdline = SamtoolsIndexCommandline(samtools_exe)
        cmdline.set_parameter("input_bam", input_bam)
        stdout, stderr = cmdline()

    def test_faidx(self):
        cmdline = SamtoolsFaidxCommandline(samtools_exe)
        cmdline.set_parameter("reference", self.reference)
        stdout, stderr = cmdline()
        self.assertFalse(stderr, f"Samtools faidx failed:\n{cmdline}\nStderr:{stderr}")
        self.assertTrue(os.path.isfile(self.referenceindexfile))

    def test_calmd(self):
        """Test for samtools calmd."""
        self.create_fasta_index()
        cmdline = SamtoolsCalmdCommandline(samtools_exe)
        cmdline.set_parameter("reference", self.reference)
        cmdline.set_parameter("input_bam", self.bamfile1)
        # If there is no index file for the reference
        # samtools calmd creates one at the time of calling

        if os.path.exists(self.referenceindexfile):
            # print("exists")
            stderr_calmd_expected = ""
        else:
            # print("doesn't exist")
            stderr_calmd_expected = "[fai_load] build FASTA index.\n"
        stdout, stderr = cmdline()
        self.assertEqual(stderr, stderr_calmd_expected)

    def test_cat(self):
        cmdline = SamtoolsCatCommandline(samtools_exe)
        cmdline.set_parameter("o", self.outbamfile)
        cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
        stdout, stderr = cmdline()
        self.assertEqual(stderr, "")

    # TODO: def test_fixmate(self):

    def test_sort(self):
        cmdline = SamtoolsVersion0xSortCommandline(samtools_exe)
        cmdline.set_parameter("input", self.bamfile1)
        cmdline.set_parameter("out_prefix", "SamBam/out")

        try:
            stdout, stderr = cmdline()
        except ApplicationError as err:
            if (
                "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files"
                in str(err)
            ):
                cmdline = SamtoolsVersion1xSortCommandline(samtools_exe)
                cmdline.set_parameter("input", self.bamfile1)
                cmdline.set_parameter("-T", "out")
                cmdline.set_parameter("-o", "out.bam")
                try:
                    stdout, stderr = cmdline()
                except ApplicationError:
                    raise
            else:
                raise
        self.assertFalse(stderr, f"Samtools sort failed:\n{cmdline}\nStderr:{stderr}")

    def test_index(self):
        cmdline = SamtoolsIndexCommandline(samtools_exe)
        cmdline.set_parameter("input_bam", self.bamfile1)
        stdout, stderr = cmdline()
        self.assertFalse(stderr, f"Samtools index failed:\n{cmdline}\nStderr:{stderr}")
        self.assertTrue(os.path.exists(self.bamindexfile1))

    def test_idxstats(self):
        self.create_bam_index(self.bamfile1)
        cmdline = SamtoolsIdxstatsCommandline(samtools_exe)
        cmdline.set_parameter("input_bam", self.bamfile1)
        stdout, stderr = cmdline()
        self.assertFalse(
            stderr, f"Samtools idxstats failed:\n{cmdline}\nStderr:{stderr}"
        )

    def test_merge(self):
        cmdline = SamtoolsMergeCommandline(samtools_exe)
        cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
        cmdline.set_parameter("out_bam", self.outbamfile)
        cmdline.set_parameter("f", True)  # Overwrite out.bam if it exists
        stdout, stderr = cmdline()
        # Worked up to v1.2, then there was a regression failing with message
        # but as of v1.3 expect a warning: [W::bam_merge_core2] No @HD tag found.
        self.assertTrue(
            not stderr or stderr.strip() == "[W::bam_merge_core2] No @HD tag found.",
            f"Samtools merge failed:\n{cmdline}\nStderr:{stderr}",
        )
        self.assertTrue(os.path.exists(self.outbamfile))

    def test_mpileup(self):
        cmdline = SamtoolsMpileupCommandline(samtools_exe)
        cmdline.set_parameter("input_file", [self.bamfile1])
        stdout, stderr = cmdline()
        self.assertNotIn("[bam_pileup_core]", stdout)

    def test_mpileup_list(self):
        cmdline = SamtoolsMpileupCommandline(samtools_exe)
        cmdline.set_parameter("input_file", [self.sortedbamfile1, self.sortedbamfile2])
        stdout, stderr = cmdline()
        self.assertNotIn("[bam_pileup_core]", stdout)

    # TODO: def test_phase(self):
    # TODO: def test_reheader(self):
    # TODO: def test_rmdup(self):
    # TODO: def test_targetcut(self):


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
