def assign_genotype_to_variant(variant, sample, genotype_result):
variant_id = genotype_result['variant.id']
sample_name = genotype_result['sample.name']
outcome = genotype_result['genotype']
if (variant.var_id != variant_id) or (sample.name != sample_name):
msg = ("Error: assign_genotype: "
"Variant/Sample ({}/{}) to genotype result ({}/{}) "
"mismatch!").format(variant.var_id, sample.name, variant_id, sample_name)
die(msg)
if bool(outcome) is False:
variant.genotype(sample.name).set_format('GT', './.')
else:
variant.qual += outcome['qual']
variant.genotype(sample.name).set_format('GT', outcome['formats']['GT'])
variant.genotype(sample.name).set_format('GQ', outcome['formats']['GQ'])
variant.genotype(sample.name).set_format('SQ', outcome['formats']['SQ'])
variant.genotype(sample.name).set_format('GL', outcome['formats']['GL'])
variant.genotype(sample.name).set_format('DP', outcome['formats']['DP'])
variant.genotype(sample.name).set_format('AO', outcome['formats']['AO'])
variant.genotype(sample.name).set_format('RO', outcome['formats']['RO'])
# if detailed:
variant.genotype(sample.name).set_format('AS', outcome['formats']['AS'])
variant.genotype(sample.name).set_format('ASC', outcome['formats']['ASC'])
variant.genotype(sample.name).set_format('RS', outcome['formats']['RS'])
variant.genotype(sample.name).set_format('AP', outcome['formats']['AP'])
variant.genotype(sample.name).set_format('RP', outcome['formats']['RP'])
variant.genotype(sample.name).set_format('QR', outcome['formats']['QR'])
variant.genotype(sample.name).set_format('QA', outcome['formats']['QA'])
variant.genotype(sample.name).set_format('AB', outcome['formats']['AB'])
return variant
def open_alignment_file(afile, reference_fasta):
fd = None
if afile.endswith('.bam'):
fd = pysam.AlignmentFile(afile, mode='rb')
elif afile.endswith('.cram'):
fd = pysam.AlignmentFile(afile, mode='rc', reference_filename=reference_fasta)
else:
die('Error: %s is not a valid alignment file (*.bam or *.cram)\n' % afile)
return fd
def open_alignment_file(afile, reference_fasta):
fd = None
if afile.endswith('.bam'.encode('ascii')):
fd = pysam.AlignmentFile(afile, mode='rb')
elif afile.endswith('.cram'.encode('ascii')):
fd = pysam.AlignmentFile(afile,
mode='rc',
reference_filename=reference_fasta)
else:
die('Error: %s is not a valid alignment file (*.bam or *.cram)\n' %
afile)
return fd
def assign_genotype_to_variant(variant, sample, genotype_result):
variant_id = genotype_result['variant.id']
sample_name = genotype_result['sample.name']
outcome = genotype_result['genotype']
if (variant.var_id != variant_id) or (sample.name != sample_name):
msg = ("Error: assign_genotype: "
"Variant/Sample ({}/{}) to genotype result ({}/{}) "
"mismatch!").format(variant.var_id, sample.name, variant_id,
sample_name)
die(msg)
if bool(outcome) is False:
variant.genotype(sample.name).set_format('GT', './.')
else:
variant.qual += outcome['qual']
variant.genotype(sample.name).set_format('GT',
outcome['formats']['GT'])
variant.genotype(sample.name).set_format('GQ',
outcome['formats']['GQ'])
variant.genotype(sample.name).set_format('SQ',
outcome['formats']['SQ'])
variant.genotype(sample.name).set_format('GL',
outcome['formats']['GL'])
variant.genotype(sample.name).set_format('DP',
outcome['formats']['DP'])
variant.genotype(sample.name).set_format('AO',
outcome['formats']['AO'])
variant.genotype(sample.name).set_format('RO',
outcome['formats']['RO'])
# if detailed:
variant.genotype(sample.name).set_format('AS',
outcome['formats']['AS'])
variant.genotype(sample.name).set_format('ASC',
outcome['formats']['ASC'])
variant.genotype(sample.name).set_format('RS',
outcome['formats']['RS'])
variant.genotype(sample.name).set_format('AP',
outcome['formats']['AP'])
variant.genotype(sample.name).set_format('RP',
outcome['formats']['RP'])
variant.genotype(sample.name).set_format('QR',
outcome['formats']['QR'])
variant.genotype(sample.name).set_format('QA',
outcome['formats']['QA'])
variant.genotype(sample.name).set_format('AB',
outcome['formats']['AB'])
return variant
def ensure_valid_alignment_file(afile):
if not (afile.endswith('.bam'.encode('ascii'))
or afile.endswith('.cram'.encode('ascii'))):
die('Error: %s is not a valid alignment file (*.bam or *.cram)\n' %
afile)
def ensure_valid_alignment_file(afile):
if not (afile.endswith('.bam') or afile.endswith('.cram')):
die('Error: %s is not a valid alignment file (*.bam or *.cram)\n' % afile)