def test_all_stepper(self):
refs = force_str(
pysam.samtools.mpileup("-f", self.fastafilename, "-A", "-B",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="all", fastafile=self.fastafile)
self.check_equal(refs, iterator)
def test_samtools_stepper(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename,
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile)
self.check_equal(refs, iterator)
def test_samtools_stepper_redo_baq(self):
refs = force_str(
pysam.samtools.mpileup("-f", self.fastafilename, "--redo-BAQ",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
redo_baq=True)
self.check_equal(refs, iterator)
def test_samtools_stepper_ignore_orphans(self):
refs = force_str(
pysam.samtools.mpileup("-f", self.fastafilename, "--count-orphans",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
ignore_orphans=False)
self.check_equal(refs, iterator)
def test_samtools_stepper_base_quality_threshold(self):
refs = force_str(
pysam.samtools.mpileup("-f", self.fastafilename, "--min-BQ", "20",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
min_base_quality=20)
self.check_equal(refs, iterator)
def build_mapping_qualities_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
with subprocess.Popen(["samtools", "mpileup", "-s", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=FNULL) as proc:
data = [force_str(x).split()[6] for x in proc.stdout.readlines()]
return data
def test_samtools_stepper_mapping_quality_threshold(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename, "--min-MQ", "15",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="samtools",
fastafile=self.fastafile,
min_mapping_quality=15)
self.check_equal(refs, iterator)
def build_query_sequences_flagfilter_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
with subprocess.Popen(["samtools", "view", "-f", "2", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=FNULL) as proc:
data = [force_str(x).split()[10] for x in proc.stdout.readlines()]
return data
def build_query_positions_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
with subprocess.Popen(["samtools", "mpileup", "-O", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=FNULL) as proc:
data = [list(map(int, force_str(x).split()[6].split(",")))
for x in proc.stdout.readlines()]
return data
def test_ignore_overlaps(self):
refs = force_str(
samtools_mpileup("-f", self.fastafilename, "-A", "-B", "-x",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(stepper="all",
fastafile=self.fastafile,
ignore_overlaps=False)
self.check_equal(refs, iterator)
def test_samtools_stepper(self):
refs = force_str(
pysam.samtools.mpileup(
"-f", self.fastafilename,
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(
stepper="samtools",
fastafile=self.fastafile)
self.check_equal(refs, iterator)
def test_samtools_stepper_ignore_orphans(self):
refs = force_str(
pysam.samtools.mpileup(
"-f", self.fastafilename,
"--count-orphans",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(
stepper="samtools",
fastafile=self.fastafile,
ignore_orphans=False)
self.check_equal(refs, iterator)
def test_samtools_stepper_base_quality_threshold(self):
refs = force_str(
pysam.samtools.mpileup(
"-f", self.fastafilename,
"--min-BQ", "20",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(
stepper="samtools",
fastafile=self.fastafile,
min_base_quality=20)
self.check_equal(refs, iterator)
def test_ignore_overlaps(self):
refs = force_str(
pysam.samtools.mpileup(
"-f", self.fastafilename,
"-A", "-B", "-x",
self.samfilename)).splitlines(True)
iterator = self.samfile.pileup(
stepper="all",
fastafile=self.fastafile,
ignore_overlaps=False)
self.check_equal(refs, iterator)
def build_query_sequences_flagfilter_with_samtoolsshell(fn):
retval = os.popen("samtools view -f 2 {} 2> /dev/null | cut -f 11".format(fn)).read()
return force_str(retval).splitlines()
