class VcfConverter(InputFileConverter):
def __init__(self, **kwargs):
InputFileConverter.__init__(self, **kwargs)
self.pass_only = kwargs.pop('pass_only', False)
self.sample_name = kwargs.pop('sample_name', None)
self.normal_sample_name = kwargs.pop('normal_sample_name', None)
self.proximal_variants_vcf = kwargs.pop('proximal_variants_vcf', None)
self.proximal_variants_tsv = kwargs.pop('proximal_variants_tsv', None)
self.peptide_length = kwargs.pop('peptide_length', None)
if self.proximal_variants_vcf and not (self.proximal_variants_tsv
and self.peptide_length):
sys.exit(
"A proximal variants TSV output path and peptide length need to be specified if a proximal variants input VCF is provided."
)
if self.proximal_variants_vcf and not lib.utils.is_gz_file(
self.input_file):
sys.exit(
"Input VCF {} needs to be bgzipped when running with a proximal variants VCF."
.format(self.input_file))
if self.proximal_variants_vcf and not lib.utils.is_gz_file(
self.proximal_variants_vcf):
sys.exit("Proximal variants VCF {} needs to be bgzipped.".format(
self.proximal_variants_vcf))
if self.proximal_variants_vcf and not os.path.exists(
self.proximal_variants_vcf + '.tbi'):
sys.exit(
'No .tbi file found for proximal variants VCF {}. Proximal variants VCF needs to be tabix indexed.'
.format(self.proximal_variants_vcf))
if self.proximal_variants_vcf and not os.path.exists(self.input_file +
'.tbi'):
sys.exit(
'No .tbi file found for input VCF {}. Input VCF needs to be tabix indexed if processing with proximal variants.'
.format(self.input_file))
if lib.utils.is_gz_file(self.input_file):
mode = 'rb'
else:
mode = 'r'
if self.proximal_variants_vcf:
self.proximal_variants_tsv_fh = open(self.proximal_variants_tsv,
'w')
self.proximal_variants_writer = csv.DictWriter(
self.proximal_variants_tsv_fh,
delimiter='\t',
fieldnames=[
'chromosome_name', 'start', 'stop', 'reference', 'variant',
'amino_acid_change', 'codon_change', 'protein_position',
'type', 'main_somatic_variant'
])
self.proximal_variants_writer.writeheader()
self.proximal_variant_parser = ProximalVariant(
self.proximal_variants_vcf, self.pass_only)
self.somatic_vcf_fh = open(self.input_file, mode)
self.somatic_vcf_reader = vcf.Reader(self.somatic_vcf_fh)
self.reader = open(self.input_file, mode)
self.vcf_reader = vcf.Reader(self.reader)
if len(self.vcf_reader.samples) > 1:
if not self.sample_name:
sys.exit(
"VCF contains more than one sample but sample_name is not set."
)
elif self.sample_name not in self.vcf_reader.samples:
sys.exit(
"sample_name {} not a sample ID in the #CHROM header of VCF {}"
.format(self.sample_name, self.input_file))
if self.normal_sample_name is not None and self.normal_sample_name not in self.vcf_reader.samples:
sys.exit(
"normal_sample_name {} not a sample ID in the #CHROM header of VCF {}"
.format(self.normal_sample_name, self.input_file))
elif len(self.vcf_reader.samples) == 0:
sys.exit("VCF doesn't contain any sample genotype information.")
else:
self.sample_name = self.vcf_reader.samples[0]
self.writer = open(self.output_file, 'w')
self.tsv_writer = csv.DictWriter(self.writer,
delimiter='\t',
fieldnames=self.output_headers(),
restval='NA')
self.tsv_writer.writeheader()
self.csq_parser = self.create_csq_parser()
if 'DownstreamProtein' not in self.csq_parser.csq_format:
sys.exit(
"VCF doesn't contain VEP DownstreamProtein annotations. Please re-annotate the VCF with VEP and the Wildtype and Downstream plugins."
)
if 'WildtypeProtein' not in self.csq_parser.csq_format:
sys.exit(
"VCF doesn't contain VEP WildtypeProtein annotations. Please re-annotate the VCF with VEP and the Wildtype and Downstream plugins."
)
def is_insertion(self, ref, alt):
return len(alt) > len(ref)
def is_deletion(self, ref, alt):
return len(alt) < len(ref)
def create_csq_parser(self):
info_fields = self.vcf_reader.infos
if 'CSQ' not in info_fields:
sys.exit(
'Input VCF does not contain a CSQ header. Please annotate the VCF with VEP before running it.'
)
if info_fields['CSQ'] is None:
sys.exit(
'Failed to extract format string from info description for tag (CSQ)'
)
else:
csq_header = info_fields['CSQ']
return CsqParser(csq_header.desc)
def resolve_consequence(self, consequence_string, ref, alt):
if '&' in consequence_string:
consequences = {
consequence.lower()
for consequence in consequence_string.split('&')
}
elif '.' in consequence_string:
consequences = {
consequence.lower()
for consequence in consequence_string.split('.')
}
else:
consequences = [consequence_string.lower()]
if 'start_lost' in consequences:
consequence = None
elif 'frameshift_variant' in consequences:
consequence = 'FS'
elif 'missense_variant' in consequences:
consequence = 'missense'
elif 'inframe_insertion' in consequences:
consequence = 'inframe_ins'
elif 'inframe_deletion' in consequences:
consequence = 'inframe_del'
elif 'protein_altering_variant' in consequences:
if len(ref) > len(alt) and (len(ref) - len(alt)) % 3 == 0:
consequence = 'inframe_del'
elif len(alt) > len(ref) and (len(alt) - len(ref)) % 3 == 0:
consequence = 'inframe_ins'
else:
consequence = None
else:
consequence = None
return consequence
def calculate_vaf(self, var_count, depth):
if depth == 0:
return 'NA'
else:
return (var_count / depth)
def get_depth_from_vcf_genotype(self, genotype, tag):
try:
depth = genotype[tag]
if depth is None or depth == "":
depth = 'NA'
except AttributeError:
depth = 'NA'
return depth
def get_vaf_from_vcf_genotype(self, genotype, alts, alt, af_tag, ad_tag,
dp_tag):
try:
allele_frequencies = genotype[af_tag]
if isinstance(allele_frequencies, list):
vaf = allele_frequencies[alts.index(alt)]
else:
vaf = allele_frequencies
if vaf > 1:
print(
"Warning: VAF is expected to be a fraction, but is larger than 1. If VAFs are encoded as percentages, please adjust the coverage cutoffs accordingly."
)
except (AttributeError, TypeError):
try:
allele_depths = genotype[ad_tag]
if isinstance(allele_depths, list):
#sometimes AF is type R, sometimes it's A
if len(allele_depths) == len(alts):
var_count = allele_depths[alts.index(alt)]
elif len(allele_depths) == len(alts) + 1:
var_count = allele_depths[alts.index(alt) + 1]
else:
print(
"Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype {}"
.format(genotype))
return 'NA'
else:
var_count = allele_depths
if var_count is None or var_count == "":
return 'NA'
depth = genotype[dp_tag]
if depth is None or depth == "":
return 'NA'
vaf = self.calculate_vaf(int(var_count), int(depth))
except AttributeError:
vaf = 'NA'
return vaf
def calculate_coverage_for_entry(self, entry, reference, alt, start,
chromosome, genotype):
coverage_for_entry = {}
coverage_for_entry['tdna_depth'] = self.get_depth_from_vcf_genotype(
genotype, 'DP')
coverage_for_entry['trna_depth'] = self.get_depth_from_vcf_genotype(
genotype, 'RDP')
alts = list(map(lambda x: str(x), entry.ALT))
coverage_for_entry['tdna_vaf'] = self.get_vaf_from_vcf_genotype(
genotype, alts, alt, 'AF', 'AD', 'DP')
coverage_for_entry['trna_vaf'] = self.get_vaf_from_vcf_genotype(
genotype, alts, alt, 'RAF', 'RAD', 'RDP')
if self.normal_sample_name is not None:
normal_genotype = entry.genotype(self.normal_sample_name)
coverage_for_entry[
'normal_depth'] = self.get_depth_from_vcf_genotype(
normal_genotype, 'DP')
coverage_for_entry['normal_vaf'] = self.get_vaf_from_vcf_genotype(
normal_genotype, alts, alt, 'AF', 'AD', 'DP')
return coverage_for_entry
def write_proximal_variant_entries(self, entry, alt, transcript_name,
index):
proximal_variants = self.proximal_variant_parser.extract(
entry, alt, transcript_name, self.peptide_length)
for (proximal_variant, csq_entry) in proximal_variants:
if len(
list(
self.somatic_vcf_reader.fetch(
proximal_variant.CHROM, proximal_variant.POS - 1,
proximal_variant.POS))) > 0:
proximal_variant_type = 'somatic'
else:
proximal_variant_type = 'germline'
if '/' in csq_entry['Protein_position']:
protein_position = csq_entry['Protein_position'].split('/')[0]
else:
protein_position = csq_entry['Protein_position']
proximal_variant_entry = {
'chromosome_name': proximal_variant.CHROM,
'start': proximal_variant.affected_start,
'stop': proximal_variant.affected_end,
'reference': proximal_variant.REF,
'variant': proximal_variant.ALT[0],
'amino_acid_change': csq_entry['Amino_acids'],
'codon_change': csq_entry['Codons'],
'protein_position': protein_position,
'type': proximal_variant_type,
'main_somatic_variant': index,
}
self.proximal_variants_writer.writerow(proximal_variant_entry)
def close_filehandles(self):
self.writer.close()
self.reader.close()
if self.proximal_variants_vcf:
self.proximal_variant_parser.fh.close()
self.proximal_variants_tsv_fh.close()
self.somatic_vcf_fh.close()
def decode_hex(self, string):
hex_string = string.group(0).replace('%', '')
return binascii.unhexlify(hex_string).decode('utf-8')
def execute(self):
indexes = []
count = 1
while True:
try:
entry = next(self.vcf_reader)
except StopIteration:
break
except ValueError as e:
raise Exception(
"VCF is truncated in the middle of an entry near string '{}'"
.format(str(e).split("'")[1]))
except IndexError as e:
raise Exception("VCF is truncated at the end of the file")
except Exception as e:
raise Exception("Error while reading VCF entry: {}".format(
str(e)))
chromosome = entry.CHROM
start = entry.affected_start
stop = entry.affected_end
reference = entry.REF
alts = entry.ALT
genotype = entry.genotype(self.sample_name)
if genotype.gt_type is None or genotype.gt_type == 0:
#The genotype is uncalled or hom_ref
continue
filt = entry.FILTER
if self.pass_only and not (filt is None or len(filt) == 0):
continue
if 'CSQ' not in entry.INFO:
continue
alleles_dict = self.csq_parser.resolve_alleles(entry)
for alt in alts:
alt = str(alt)
if genotype.gt_bases and alt not in genotype.gt_bases.split(
'/'):
continue
coverage_for_entry = self.calculate_coverage_for_entry(
entry, reference, alt, start, chromosome, genotype)
transcripts = self.csq_parser.parse_csq_entries_for_allele(
entry.INFO['CSQ'], alt)
if len(transcripts) == 0:
csq_allele = alleles_dict[alt]
transcripts = self.csq_parser.parse_csq_entries_for_allele(
entry.INFO['CSQ'], csq_allele)
if len(transcripts) == 0 and self.is_deletion(reference, alt):
transcripts = self.csq_parser.parse_csq_entries_for_allele(
entry.INFO['CSQ'], 'deletion')
for transcript in transcripts:
if '/' in transcript['Protein_position']:
protein_position = transcript[
'Protein_position'].split('/')[0]
else:
protein_position = transcript['Protein_position']
transcript_name = transcript['Feature']
consequence = self.resolve_consequence(
transcript['Consequence'], reference, alt)
if consequence is None:
continue
elif consequence == 'FS':
if transcript['DownstreamProtein'] == '':
print(
"frameshift_variant transcript does not contain a DownstreamProtein sequence. Skipping.\n{} {} {} {} {}"
.format(entry.CHROM, entry.POS, entry.REF, alt,
transcript['Feature']))
continue
else:
amino_acid_change_position = "%s%s/%s" % (
protein_position, entry.REF, alt)
else:
if transcript['Amino_acids'] == '':
print(
"Transcript does not contain Amino_acids change information. Skipping.\n{} {} {} {} {}"
.format(entry.CHROM, entry.POS, entry.REF, alt,
transcript['Feature']))
continue
else:
amino_acid_change_position = protein_position + transcript[
'Amino_acids']
gene_name = transcript['SYMBOL']
index = '%s.%s.%s.%s.%s' % (count, gene_name,
transcript_name, consequence,
amino_acid_change_position)
if index in indexes:
sys.exit(
"Warning: TSV index already exists: {}".format(
index))
else:
indexes.append(index)
count += 1
if self.proximal_variants_vcf:
self.write_proximal_variant_entries(
entry, alt, transcript_name, index)
ensembl_gene_id = transcript['Gene']
hgvsc = re.sub(
r'%[0-9|A-F][0-9|A-F]', self.decode_hex,
transcript['HGVSc']) if 'HGVSc' in transcript else 'NA'
hgvsp = re.sub(
r'%[0-9|A-F][0-9|A-F]', self.decode_hex,
transcript['HGVSp']) if 'HGVSp' in transcript else 'NA'
if 'TSL' in transcript and transcript[
'TSL'] is not None and transcript['TSL'] != '':
tsl = transcript['TSL']
else:
tsl = 'NA'
output_row = {
'chromosome_name':
entry.CHROM,
'start':
entry.affected_start,
'stop':
entry.affected_end,
'reference':
entry.REF,
'variant':
alt,
'gene_name':
gene_name,
'transcript_name':
transcript_name,
'transcript_support_level':
tsl,
'ensembl_gene_id':
ensembl_gene_id,
'hgvsc':
hgvsc,
'hgvsp':
hgvsp,
'wildtype_amino_acid_sequence':
transcript['WildtypeProtein'],
'downstream_amino_acid_sequence':
transcript['DownstreamProtein'],
'fusion_amino_acid_sequence':
'',
'variant_type':
consequence,
'protein_position':
protein_position,
'index':
index,
'protein_length_change':
transcript['ProteinLengthChange'],
}
if transcript['Amino_acids']:
output_row['amino_acid_change'] = transcript[
'Amino_acids']
if transcript['Codons']:
output_row['codon_change'] = transcript['Codons']
else:
output_row['codon_change'] = 'NA'
for (tag, key, comparison_fields) in zip(
['TX', 'GX'],
['transcript_expression', 'gene_expression'],
[[transcript_name], [ensembl_gene_id, gene_name]]):
if tag in self.vcf_reader.formats:
if tag in genotype.data._asdict():
expressions = genotype[tag]
if isinstance(expressions, list):
for expression in expressions:
(item, value) = expression.split('|')
for comparison_field in comparison_fields:
if item == comparison_field:
output_row[key] = value
elif expressions is not None:
(item, value) = expressions.split('|')
for comparison_field in comparison_fields:
if item == comparison_field:
output_row[key] = value
output_row.update(coverage_for_entry)
self.tsv_writer.writerow(output_row)
self.close_filehandles()
class VcfConverter(InputFileConverter):
def __init__(self, **kwargs):
InputFileConverter.__init__(self, **kwargs)
self.gene_expn_file = kwargs.pop('gene_expn_file', None)
self.transcript_expn_file = kwargs.pop('transcript_expn_file', None)
self.normal_snvs_coverage_file = kwargs.pop(
'normal_snvs_coverage_file', None)
self.normal_indels_coverage_file = kwargs.pop(
'normal_indels_coverage_file', None)
self.tdna_snvs_coverage_file = kwargs.pop('tdna_snvs_coverage_file',
None)
self.tdna_indels_coverage_file = kwargs.pop(
'tdna_indels_coverage_file', None)
self.trna_snvs_coverage_file = kwargs.pop('trna_snvs_coverage_file',
None)
self.trna_indels_coverage_file = kwargs.pop(
'trna_indels_coverage_file', None)
self.pass_only = kwargs.pop('pass_only', False)
self.sample_name = kwargs.pop('sample_name', None)
self.normal_sample_name = kwargs.pop('normal_sample_name', None)
self.proximal_variants_vcf = kwargs.pop('proximal_variants_vcf', None)
self.proximal_variants_tsv = kwargs.pop('proximal_variants_tsv', None)
self.peptide_length = kwargs.pop('peptide_length', None)
if self.proximal_variants_vcf and not (self.proximal_variants_tsv
and self.peptide_length):
sys.exit(
"A proximal variants TSV output path and peptide length need to be specified if a proximal variants input VCF is provided"
)
if self.proximal_variants_vcf and not os.path.exists(
self.proximal_variants_vcf + '.tbi'):
sys.exit(
'No .tbi file found for proximal variants VCF {}. Proximal variants VCF needs to be tabix indexed'
.format(self.proximal_variants_vcf))
if self.proximal_variants_vcf and not os.path.exists(self.input_file +
'.tbi'):
sys.exit(
'No .tbi file found for input VCF {}. Input VCF needs to be tabix indexed if processing with proximal variants.'
.format(self.input_file))
if lib.utils.is_gz_file(self.input_file):
mode = 'rb'
else:
mode = 'r'
if self.proximal_variants_vcf:
self.proximal_variants_tsv_fh = open(self.proximal_variants_tsv,
'w')
self.proximal_variants_writer = csv.DictWriter(
self.proximal_variants_tsv_fh,
delimiter='\t',
fieldnames=[
'chromosome_name', 'start', 'stop', 'reference', 'variant',
'amino_acid_change', 'codon_change', 'protein_position',
'type', 'main_somatic_variant'
])
self.proximal_variants_writer.writeheader()
self.proximal_variant_parser = ProximalVariant(
self.proximal_variants_vcf, self.pass_only)
self.somatic_vcf_fh = open(self.input_file, mode)
self.somatic_vcf_reader = vcf.Reader(self.somatic_vcf_fh)
self.reader = open(self.input_file, mode)
self.vcf_reader = vcf.Reader(self.reader)
if len(self.vcf_reader.samples) > 1:
if not self.sample_name:
sys.exit(
"VCF contains more than one sample but sample_name is not set."
)
elif self.sample_name not in self.vcf_reader.samples:
sys.exit("sample_name {} not in VCF {}".format(
self.sample_name, self.input_file))
if self.normal_sample_name is not None and self.normal_sample_name not in self.vcf_reader.samples:
sys.exit("normal_sample_name {} not in VCF {}".format(
self.normal_sample_name, self.input_file))
elif len(self.vcf_reader.samples) == 0:
sys.exit("VCF doesn't contain any sample genotype information.")
else:
self.sample_name = self.vcf_reader.samples[0]
self.writer = open(self.output_file, 'w')
self.tsv_writer = csv.DictWriter(self.writer,
delimiter='\t',
fieldnames=self.output_headers(),
restval='NA')
self.tsv_writer.writeheader()
self.csq_parser = self.create_csq_parser()
def parse_bam_readcount_file(self, bam_readcount_file):
with open(bam_readcount_file, 'r') as reader:
coverage_tsv_reader = csv.reader(reader, delimiter='\t')
coverage = {}
for row in coverage_tsv_reader:
chromosome = row[0]
position = row[1]
reference_base = row[2].upper()
depth = row[3]
brct = row[4:]
if chromosome not in coverage:
coverage[chromosome] = {}
if position not in coverage[chromosome]:
coverage[chromosome][position] = {}
coverage[chromosome][position][
reference_base] = self.parse_brct_field(brct)
coverage[chromosome][position][reference_base]['depth'] = depth
return coverage
def parse_brct_field(self, brct_entry):
parsed_brct = {}
for brct in brct_entry:
(base, count, rest) = brct.split(':', 2)
parsed_brct[base.upper()] = count
return parsed_brct
def is_insertion(self, ref, alt):
return len(alt) > len(ref)
def is_deletion(self, ref, alt):
return len(alt) < len(ref)
def simplify_indel_allele(self, ref, alt):
while len(ref) > 0 and len(alt) > 0 and ref[-1] == alt[-1]:
ref = ref[0:-1]
alt = alt[0:-1]
while len(ref) > 0 and len(alt) > 0 and ref[0] == alt[0]:
ref = ref[1:]
alt = alt[1:]
return ref, alt
def create_csq_parser(self):
info_fields = self.vcf_reader.infos
if 'CSQ' not in info_fields:
sys.exit(
'Input VCF does not contain a CSQ header. Please annotate the VCF with VEP before running it.'
)
if info_fields['CSQ'] is None:
sys.exit(
'Failed to extract format string from info description for tag (CSQ)'
)
else:
csq_header = info_fields['CSQ']
return CsqParser(csq_header.desc)
def resolve_consequence(self, consequence_string):
if '&' in consequence_string:
consequences = {
consequence.lower()
for consequence in consequence_string.split('&')
}
elif '.' in consequence_string:
consequences = {
consequence.lower()
for consequence in consequence_string.split('.')
}
else:
consequences = [consequence_string.lower()]
if 'start_lost' in consequences:
consequence = None
elif 'frameshift_variant' in consequences:
consequence = 'FS'
elif 'missense_variant' in consequences:
consequence = 'missense'
elif 'inframe_insertion' in consequences:
consequence = 'inframe_ins'
elif 'inframe_deletion' in consequences:
consequence = 'inframe_del'
else:
consequence = None
return consequence
def calculate_vaf(self, var_count, depth):
if depth == 0:
return 'NA'
else:
return (var_count / depth)
def parse_gene_expns_file(self):
gene_expns = {}
if self.gene_expn_file is not None:
with open(self.gene_expn_file, 'r') as reader:
genes_tsv_reader = csv.DictReader(reader, delimiter='\t')
for row in genes_tsv_reader:
if row['tracking_id'] not in gene_expns.keys():
gene_expns[row['tracking_id']] = {}
gene_expns[row['tracking_id']][row['locus']] = row
return gene_expns
def parse_transcript_expns_file(self):
transcript_expns = {}
if self.transcript_expn_file is not None:
with open(self.transcript_expn_file, 'r') as reader:
isoforms_tsv_reader = csv.DictReader(reader, delimiter='\t')
for row in isoforms_tsv_reader:
transcript_expns[row['tracking_id']] = row
return transcript_expns
def parse_coverage_files(self):
coverage = {}
for variant_type in ['snvs', 'indels']:
for data_type in ['normal', 'tdna', 'trna']:
coverage_file_name = '_'.join(
[data_type, variant_type, 'coverage_file'])
coverage_file = getattr(self, coverage_file_name)
if coverage_file is not None:
if variant_type not in coverage:
coverage[variant_type] = {}
coverage[variant_type][
data_type] = self.parse_bam_readcount_file(
coverage_file)
return coverage
def determine_bam_readcount_bases(self, entry, reference, alt, start):
if len(reference) == len(alt):
bam_readcount_position = entry.POS
variant_type = 'snvs'
ref_base = reference
var_base = alt
else:
if self.is_deletion(reference, alt):
bam_readcount_position = start + 1
(simplified_reference,
simplified_alt) = self.simplify_indel_allele(reference, alt)
ref_base = reference[1:2]
var_base = '-' + simplified_reference
elif self.is_insertion(reference, alt):
bam_readcount_position = start
(simplified_reference,
simplified_alt) = self.simplify_indel_allele(reference, alt)
ref_base = reference
var_base = '+' + simplified_alt
variant_type = 'indels'
return (bam_readcount_position, ref_base, var_base, variant_type)
def get_depth_from_vcf_genotype(self, genotype, tag):
try:
depth = genotype[tag]
if depth is None or depth == "":
depth = 'NA'
except AttributeError:
depth = 'NA'
return depth
def get_vaf_from_vcf_genotype(self, genotype, alts, alt, af_tag, ad_tag,
dp_tag):
try:
allele_frequencies = genotype[af_tag]
if isinstance(allele_frequencies, list):
vaf = allele_frequencies[alts.index(alt)]
else:
vaf = allele_frequencies
if vaf > 1:
print(
"Warning: VAF is expected to be a fraction, but is larger than 1. If VAFs are encoded as percentages, please adjust the coverage cutoffs accordingly."
)
except (AttributeError, TypeError):
try:
allele_depths = genotype[ad_tag]
if isinstance(allele_depths, list):
#sometimes AF is type R, sometimes it's A
if len(allele_depths) == len(alts):
var_count = allele_depths[alts.index(alt)]
elif len(allele_depths) == len(alts) + 1:
var_count = allele_depths[alts.index(alt) + 1]
else:
print(
"Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype {}"
.format(genotype))
return 'NA'
else:
var_count = allele_depths
if var_count is None or var_count == "":
return 'NA'
depth = genotype[dp_tag]
if depth is None or depth == "":
return 'NA'
vaf = self.calculate_vaf(int(var_count), int(depth))
except AttributeError:
vaf = 'NA'
return vaf
def calculate_coverage_for_entry(self, coverage, entry, reference, alt,
start, chromosome, genotype):
(bam_readcount_position, ref_base, var_base,
variant_type) = self.determine_bam_readcount_bases(
entry, reference, alt, start)
coverage_for_entry = {}
if variant_type in coverage:
for coverage_type in coverage[variant_type]:
if (chromosome in coverage[variant_type][coverage_type]
and str(bam_readcount_position)
in coverage[variant_type][coverage_type][chromosome]
and ref_base in coverage[variant_type][coverage_type]
[chromosome][str(bam_readcount_position)]):
brct = coverage[variant_type][coverage_type][chromosome][
str(bam_readcount_position)][ref_base]
if 'depth' in brct and var_base in brct:
coverage_for_entry[coverage_type + '_depth'] = int(
brct['depth'])
coverage_for_entry[coverage_type +
'_vaf'] = self.calculate_vaf(
int(brct[var_base]),
int(brct['depth']))
else:
coverage_for_entry[
'tdna_depth'] = self.get_depth_from_vcf_genotype(
genotype, 'DP')
coverage_for_entry[
'trna_depth'] = self.get_depth_from_vcf_genotype(
genotype, 'RDP')
coverage_for_entry['tdna_vaf'] = self.get_vaf_from_vcf_genotype(
genotype, entry.ALT, alt, 'AF', 'AD', 'DP')
coverage_for_entry['trna_vaf'] = self.get_vaf_from_vcf_genotype(
genotype, entry.ALT, alt, 'RAF', 'RAD', 'RDP')
if self.normal_sample_name is not None:
normal_genotype = entry.genotype(self.normal_sample_name)
coverage_for_entry[
'normal_depth'] = self.get_depth_from_vcf_genotype(
normal_genotype, 'DP')
coverage_for_entry[
'normal_vaf'] = self.get_vaf_from_vcf_genotype(
normal_genotype, entry.ALT, alt, 'AF', 'AD', 'DP')
return coverage_for_entry
def write_proximal_variant_entries(self, entry, alt, transcript_name,
index):
proximal_variants = self.proximal_variant_parser.extract(
entry, alt, transcript_name, self.peptide_length)
for (proximal_variant, csq_entry) in proximal_variants:
if len(
list(
self.somatic_vcf_reader.fetch(
proximal_variant.CHROM, proximal_variant.POS - 1,
proximal_variant.POS))) > 0:
proximal_variant_type = 'somatic'
else:
proximal_variant_type = 'germline'
proximal_variant_entry = {
'chromosome_name': proximal_variant.CHROM,
'start': proximal_variant.affected_start,
'stop': proximal_variant.affected_end,
'reference': proximal_variant.REF,
'variant': proximal_variant.ALT[0],
'amino_acid_change': csq_entry['Amino_acids'],
'codon_change': csq_entry['Codons'],
'protein_position': csq_entry['Protein_position'],
'type': proximal_variant_type,
'main_somatic_variant': index,
}
self.proximal_variants_writer.writerow(proximal_variant_entry)
def close_filehandles(self):
self.writer.close()
self.reader.close()
if self.proximal_variants_vcf:
self.proximal_variant_parser.fh.close()
self.proximal_variants_tsv_fh.close()
self.somatic_vcf_fh.close()
def decode_hex(self, string):
hex_string = string.group(0).replace('%', '')
return binascii.unhexlify(hex_string).decode('utf-8')
def execute(self):
gene_expns = self.parse_gene_expns_file()
transcript_expns = self.parse_transcript_expns_file()
coverage = self.parse_coverage_files()
indexes = []
count = 1
for entry in self.vcf_reader:
chromosome = entry.CHROM
start = entry.affected_start
stop = entry.affected_end
reference = entry.REF
alts = entry.ALT
genotype = entry.genotype(self.sample_name)
if genotype.gt_type is None or genotype.gt_type == 0:
#The genotype is uncalled or hom_ref
continue
filt = entry.FILTER
if self.pass_only and not (filt is None or len(filt) == 0):
continue
if 'CSQ' not in entry.INFO:
continue
alleles_dict = self.csq_parser.resolve_alleles(entry)
for alt in alts:
alt = str(alt)
if genotype.gt_bases and alt not in genotype.gt_bases.split(
'/'):
continue
coverage_for_entry = self.calculate_coverage_for_entry(
coverage, entry, reference, alt, start, chromosome,
genotype)
transcripts = self.csq_parser.parse_csq_entries_for_allele(
entry.INFO['CSQ'], alt)
if len(transcripts) == 0:
csq_allele = alleles_dict[alt]
transcripts = self.csq_parser.parse_csq_entries_for_allele(
entry.INFO['CSQ'], csq_allele)
if len(transcripts) == 0 and self.is_deletion(reference, alt):
transcripts = self.csq_parser.parse_csq_entries_for_allele(
entry.INFO['CSQ'], 'deletion')
for transcript in transcripts:
transcript_name = transcript['Feature']
consequence = self.resolve_consequence(
transcript['Consequence'])
if consequence is None:
continue
elif consequence == 'FS':
if transcript['DownstreamProtein'] == '':
print(
"frameshift_variant transcript does not contain a DownstreamProtein sequence. Skipping.\n{} {} {} {} {}"
.format(entry.CHROM, entry.POS, entry.REF, alt,
transcript['Feature']))
continue
else:
amino_acid_change_position = "%s%s/%s" % (
transcript['Protein_position'], entry.REF, alt)
else:
if transcript['Amino_acids'] == '':
print(
"Transcript does not contain Amino_acids change information. Skipping.\n{} {} {} {} {}"
.format(entry.CHROM, entry.POS, entry.REF, alt,
transcript['Feature']))
continue
else:
amino_acid_change_position = transcript[
'Protein_position'] + transcript['Amino_acids']
gene_name = transcript['SYMBOL']
index = '%s.%s.%s.%s.%s' % (count, gene_name,
transcript_name, consequence,
amino_acid_change_position)
if index in indexes:
sys.exit(
"Warning: TSV index already exists: {}".format(
index))
else:
indexes.append(index)
count += 1
if self.proximal_variants_vcf:
self.write_proximal_variant_entries(
entry, alt, transcript_name, index)
ensembl_gene_id = transcript['Gene']
hgvsc = re.sub(
r'%[0-9|A-F][0-9|A-F]', self.decode_hex,
transcript['HGVSc']) if 'HGVSc' in transcript else 'NA'
hgvsp = re.sub(
r'%[0-9|A-F][0-9|A-F]', self.decode_hex,
transcript['HGVSp']) if 'HGVSp' in transcript else 'NA'
if 'TSL' in transcript and transcript[
'TSL'] is not None and transcript['TSL'] != '':
tsl = transcript['TSL']
else:
tsl = 'NA'
output_row = {
'chromosome_name':
entry.CHROM,
'start':
entry.affected_start,
'stop':
entry.affected_end,
'reference':
entry.REF,
'variant':
alt,
'gene_name':
gene_name,
'transcript_name':
transcript_name,
'transcript_support_level':
tsl,
'ensembl_gene_id':
ensembl_gene_id,
'hgvsc':
hgvsc,
'hgvsp':
hgvsp,
'wildtype_amino_acid_sequence':
transcript['WildtypeProtein'],
'downstream_amino_acid_sequence':
transcript['DownstreamProtein'],
'fusion_amino_acid_sequence':
'',
'variant_type':
consequence,
'protein_position':
transcript['Protein_position'],
'index':
index,
'protein_length_change':
transcript['ProteinLengthChange'],
}
if transcript['Amino_acids']:
output_row['amino_acid_change'] = transcript[
'Amino_acids']
if transcript['Codons']:
output_row['codon_change'] = transcript['Codons']
else:
output_row['codon_change'] = 'NA'
if transcript_name in transcript_expns.keys():
transcript_expn_entry = transcript_expns[
transcript_name]
output_row[
'transcript_expression'] = transcript_expn_entry[
'FPKM']
elif 'TX' in self.vcf_reader.formats:
if 'TX' in genotype.data._asdict():
transcript_expressions = genotype['TX']
if isinstance(transcript_expressions, list):
for transcript_expression in transcript_expressions:
(transcript,
value) = transcript_expression.split('|')
if transcript == transcript_name:
output_row[
'transcript_expression'] = value
else:
(transcript,
value) = transcript_expressions.split('|')
if transcript == transcript_name:
output_row['transcript_expression'] = value
if ensembl_gene_id in gene_expns.keys():
gene_expn_entries = gene_expns[ensembl_gene_id]
gene_fpkm = 0
for locus, gene_expn_entry in gene_expn_entries.items(
):
gene_fpkm += float(gene_expn_entry['FPKM'])
output_row['gene_expression'] = gene_fpkm
elif 'GX' in self.vcf_reader.formats:
if 'GX' in genotype.data._asdict():
gene_expressions = genotype['GX']
if isinstance(gene_expressions, list):
for gene_expression in gene_expressions:
(gene, value) = gene_expression.split('|')
if ensembl_gene_id == gene or gene_name == gene:
output_row['gene_expression'] = value
else:
(gene, value) = gene_expressions.split('|')
if ensembl_gene_id == gene or gene_name == gene:
output_row['gene_expression'] = value
output_row.update(coverage_for_entry)
self.tsv_writer.writerow(output_row)
self.close_filehandles()