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# 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)]
from Bio import MissingExternalDependencyError
import sys
import os
import unittest
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 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
#################################################################
# 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 Bio._py3k 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(""),
"SAM file viewing failed: \n%s\nStdout:%s"
% (cmdline, 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"),
"SAM file viewing failed:\n%s\nStderr:%s"
% (cmdline, stderr_sam))
def create_fasta_index(self):
"""Creates 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):
"""Creates 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,
"Samtools faidx failed:\n%s\nStderr:%s"
% (cmdline, 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("doesnt 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 = SamtoolsSortCommandline(samtools_exe)
cmdline.set_parameter("input_bam", 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):
# TODO: The samtools sort API changed...
return
else:
raise
self.assertFalse(stderr,
"Samtools sort failed:\n%s\nStderr:%s"
% (cmdline, stderr))
def test_index(self):
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
stdout, stderr = cmdline()
self.assertFalse(stderr,
"Samtools index failed:\n%s\nStderr:%s"
% (cmdline, 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,
"Samtools idxstats failed:\n%s\nStderr:%s"
% (cmdline, 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.",
"Samtools merge failed:\n%s\nStderr:%s"
% (cmdline, 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.assertFalse("[bam_pileup_core]" in stdout)
def test_mpileup_list(self):
cmdline = SamtoolsMpileupCommandline(samtools_exe)
cmdline.set_parameter("input_file", [self.sortedbamfile1, self.sortedbamfile2])
stdout, stderr = cmdline()
self.assertFalse("[bam_pileup_core]" in 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)
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