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()