def get_header(header_lines = None):
"""Initiate a HeaderParser and return it"""
header_parser = HeaderParser()
if not header_lines:
header_lines = [
'##fileformat=VCFv4.2',
'##FILTER=<ID=LowQual,Description="Low quality">',
'##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">',
'##INFO=<ID=SQ,Number=G,Type=Float,Description="Just for test">',
'##INFO=<ID=CNT,Number=A,Type=Integer,Description="Number of times '\
'this allele was found in external db">',
'##contig=<ID=1,length=249250621,assembly=b37>',
'##INFO=<ID=DP_HIST,Number=R,Type=String,Description="Histogram for '\
'DP; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|'\
'62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">',
'##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for'\
' the ref and alt alleles in the order listed">',
'##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=GQ,Number=1,Type=String,Description="GenotypeQuality">'
'##reference=file:///human_g1k_v37.fasta',
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tproband'
]
for line in header_lines:
if line.startswith('##'):
header_parser.parse_meta_data(line)
elif line.startswith('#'):
header_parser.parse_header_line(line)
return header_parser
def test_vep_columns():
"""
Test how the vep columns are parsed
"""
header_parser = HeaderParser()
vep_info_line = '##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence'\
' type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence">'
header_parser.parse_meta_data(vep_info_line)
assert header_parser.vep_columns == [
'Allele', 'Gene', 'Feature', 'Feature_type', 'Consequence'
]
def test_parse_vcf_lines():
"""
Test how the header parser behaves with simple vcf lines
"""
header_parser = HeaderParser()
header_lines = [
'##fileformat=VCFv4.2',
'##FILTER=<ID=LowQual,Description="Low quality">',
'##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">',
'##INFO=<ID=CNT,Number=A,Type=Integer,Description="Number of times '\
'this allele was found in external db">',
'##contig=<ID=1,length=249250621,assembly=b37>',
'##INFO=<ID=DP_HIST,Number=R,Type=String,Description="Histogram for '\
'DP; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|'\
'62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">',
'##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for'\
' the ref and alt alleles in the order listed">',
'##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=GQ,Number=1,Type=String,Description="GenotypeQuality">'
'##reference=file:///human_g1k_v37.fasta',
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tproband'
]
for line in header_lines:
if line.startswith('##'):
header_parser.parse_meta_data(line)
elif line.startswith('#'):
header_parser.parse_header_line(line)
assert header_parser.fileformat == "VCFv4.2"
assert header_parser.individuals == ['father','mother','proband']
assert header_parser.vep_columns == []
assert "MQ" in header_parser.extra_info
assert header_parser.extra_info["MQ"]['Description'] == "RMS Mapping Quality"
assert header_parser.extra_info["CNT"]['Number'] == "A"
assert header_parser.extra_info["CNT"]['Type'] == "Integer"
assert "CNT" in header_parser.extra_info
assert "DP_HIST" in header_parser.extra_info
assert "LowQual" in header_parser.filter_dict
assert "1" in header_parser.contig_dict
assert header_parser.header == [
'CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT',
'father','mother','proband'
]
def test_vep_columns():
"""
Test how the vep columns are parsed
"""
header_parser = HeaderParser()
vep_info_line = '##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence'\
' type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence">'
header_parser.parse_meta_data(vep_info_line)
assert header_parser.vep_columns == ['Allele','Gene','Feature','Feature_type','Consequence']
def get_header(header_lines=None):
"""Initiate a HeaderParser and return it"""
header_parser = HeaderParser()
if not header_lines:
header_lines = [
'##fileformat=VCFv4.2',
'##FILTER=<ID=LowQual,Description="Low quality">',
'##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">',
'##INFO=<ID=SQ,Number=G,Type=Float,Description="Just for test">',
'##INFO=<ID=CNT,Number=A,Type=Integer,Description="Number of times '\
'this allele was found in external db">',
'##contig=<ID=1,length=249250621,assembly=b37>',
'##INFO=<ID=DP_HIST,Number=R,Type=String,Description="Histogram for '\
'DP; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|'\
'62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">',
'##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for'\
' the ref and alt alleles in the order listed">',
'##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=GQ,Number=1,Type=String,Description="GenotypeQuality">'
'##reference=file:///human_g1k_v37.fasta',
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tproband'
]
for line in header_lines:
if line.startswith('##'):
header_parser.parse_meta_data(line)
elif line.startswith('#'):
header_parser.parse_header_line(line)
return header_parser
def test_malformed_lines():
"""
Test how the header parser behaves with simple vcf lines
"""
header_parser = HeaderParser()
malformed_fileformat = '##fileformat'
malformed_info_line = '##INFO=<ID=MQ,Number=1,Description="RMS Mapping Quality">'
malformed_contig_line = '##contig=<ID=1,assembly=b37>'
with pytest.raises(SyntaxError):
header_parser.parse_meta_data(malformed_fileformat)
with pytest.raises(SyntaxError):
header_parser.parse_meta_data(malformed_info_line)
with pytest.raises(SyntaxError):
header_parser.parse_meta_data(malformed_contig_line)
def test_parse_vcf_lines():
"""
Test how the header parser behaves with simple vcf lines
"""
header_parser = HeaderParser()
header_lines = [
'##fileformat=VCFv4.2',
'##FILTER=<ID=LowQual,Description="Low quality">',
'##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">',
'##INFO=<ID=CNT,Number=A,Type=Integer,Description="Number of times '\
'this allele was found in external db">',
'##contig=<ID=1,length=249250621,assembly=b37>',
'##INFO=<ID=DP_HIST,Number=R,Type=String,Description="Histogram for '\
'DP; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|'\
'62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">',
'##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for'\
' the ref and alt alleles in the order listed">',
'##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=GQ,Number=1,Type=String,Description="GenotypeQuality">'
'##reference=file:///human_g1k_v37.fasta',
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfather\tmother\tproband'
]
for line in header_lines:
if line.startswith('##'):
header_parser.parse_meta_data(line)
elif line.startswith('#'):
header_parser.parse_header_line(line)
assert header_parser.fileformat == "VCFv4.2"
assert header_parser.individuals == ['father', 'mother', 'proband']
assert header_parser.vep_columns == []
assert "MQ" in header_parser.extra_info
assert header_parser.extra_info["MQ"][
'Description'] == "RMS Mapping Quality"
assert header_parser.extra_info["CNT"]['Number'] == "A"
assert header_parser.extra_info["CNT"]['Type'] == "Integer"
assert "CNT" in header_parser.extra_info
assert "DP_HIST" in header_parser.extra_info
assert "LowQual" in header_parser.filter_dict
assert "1" in header_parser.contig_dict
assert header_parser.header == [
'CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT',
'father', 'mother', 'proband'
]
def test_malformed_lines():
"""
Test how the header parser behaves with simple vcf lines
"""
header_parser = HeaderParser()
malformed_fileformat = '##fileformat'
malformed_info_line = '##INFO=<ID=MQ,Number=1,Description="RMS Mapping Quality">'
malformed_contig_line = '##contig=<ID=1,assembly=b37>'
with pytest.raises(SyntaxError):
header_parser.parse_meta_data(malformed_fileformat)
with pytest.raises(SyntaxError):
header_parser.parse_meta_data(malformed_info_line)
with pytest.raises(SyntaxError):
header_parser.parse_meta_data(malformed_contig_line)
def __init__(self,
infile=None,
fsock=None,
split_variants=False,
check_info=False,
allele_symbol='0',
fileformat=None):
super(VCFParser, self).__init__()
self.logger = logging.getLogger(__name__)
self.vcf = None
self.logger.debug("Set self.vcf to:{0}".format(self.vcf))
self.beginning = True
self.infile = infile
self.fsock = fsock
self.split_variants = split_variants
self.logger.info("Split variants = {0}".format(self.split_variants))
self.fileformat = fileformat
self.check_info = check_info
self.logger.info("check info = {0}".format(self.check_info))
self.allele_symbol = allele_symbol
self.logger.info("Allele symbol = {0}".format(self.allele_symbol))
self.logger.info("Initializing HeaderParser")
self.metadata = HeaderParser()
# These are the individuals described in the header
self.individuals = []
# This is the header line of the vcf
self.header = []
# If there are no file or stream the user can add variants manually.
# These will be added to self.variants
self.variants = []
if (fsock or infile):
if fsock:
if not infile and hasattr(fsock, 'name'):
self.logger.info("Reading vcf form stdin")
if sys.version_info < (3, 0):
self.logger.info("Using codecs to read stdin")
sys.stdin = getreader('utf-8')(fsock)
self.vcf = sys.stdin
else:
self.logger.info("Reading vcf form file {0}".format(infile))
file_name, file_extension = os.path.splitext(infile)
if file_extension == '.gz':
self.logger.debug("Vcf is zipped")
self.vcf = getreader('utf-8')(gzip.open(infile),
errors='replace')
elif file_extension == '.vcf':
self.vcf = open(infile,
mode='r',
encoding='utf-8',
errors='replace')
else:
raise IOError("File is not in a supported format!\n"
" Or use correct ending(.vcf or .vcf.gz)")
self.logger.debug("Reading first line.")
self.next_line = self.vcf.readline().rstrip()
self.current_line = self.next_line
# First line is allways a metadata line
if not self.next_line.startswith('#'):
raise IOError(
"VCF files allways have to start with a metadata line.")
self.metadata.parse_meta_data(self.next_line)
# Parse the metadata lines
while self.next_line.startswith('#'):
if self.next_line.startswith('##'):
self.metadata.parse_meta_data(self.next_line)
elif self.next_line.startswith('#'):
self.metadata.parse_header_line(self.next_line)
self.next_line = self.vcf.readline().rstrip()
self.individuals = self.metadata.individuals
self.logger.info("Setting self.individuals to {0}".format(
self.individuals))
self.header = self.metadata.header
self.vep_header = self.metadata.vep_columns
else:
if not self.fileformat:
raise IOError("Please initialize with a fileformat.")
else:
self.metadata.fileformat = self.fileformat
class VCFParser(object):
"""docstring for VCFParser"""
def __init__(self,
infile=None,
fsock=None,
split_variants=False,
check_info=False,
allele_symbol='0',
fileformat=None):
super(VCFParser, self).__init__()
self.logger = logging.getLogger(__name__)
self.vcf = None
self.logger.debug("Set self.vcf to:{0}".format(self.vcf))
self.beginning = True
self.infile = infile
self.fsock = fsock
self.split_variants = split_variants
self.logger.info("Split variants = {0}".format(self.split_variants))
self.fileformat = fileformat
self.check_info = check_info
self.logger.info("check info = {0}".format(self.check_info))
self.allele_symbol = allele_symbol
self.logger.info("Allele symbol = {0}".format(self.allele_symbol))
self.logger.info("Initializing HeaderParser")
self.metadata = HeaderParser()
# These are the individuals described in the header
self.individuals = []
# This is the header line of the vcf
self.header = []
# If there are no file or stream the user can add variants manually.
# These will be added to self.variants
self.variants = []
if (fsock or infile):
if fsock:
if not infile and hasattr(fsock, 'name'):
self.logger.info("Reading vcf form stdin")
if sys.version_info < (3, 0):
self.logger.info("Using codecs to read stdin")
sys.stdin = getreader('utf-8')(fsock)
self.vcf = sys.stdin
else:
self.logger.info("Reading vcf form file {0}".format(infile))
file_name, file_extension = os.path.splitext(infile)
if file_extension == '.gz':
self.logger.debug("Vcf is zipped")
self.vcf = getreader('utf-8')(gzip.open(infile),
errors='replace')
elif file_extension == '.vcf':
self.vcf = open(infile,
mode='r',
encoding='utf-8',
errors='replace')
else:
raise IOError("File is not in a supported format!\n"
" Or use correct ending(.vcf or .vcf.gz)")
self.logger.debug("Reading first line.")
self.next_line = self.vcf.readline().rstrip()
self.current_line = self.next_line
# First line is allways a metadata line
if not self.next_line.startswith('#'):
raise IOError(
"VCF files allways have to start with a metadata line.")
self.metadata.parse_meta_data(self.next_line)
# Parse the metadata lines
while self.next_line.startswith('#'):
if self.next_line.startswith('##'):
self.metadata.parse_meta_data(self.next_line)
elif self.next_line.startswith('#'):
self.metadata.parse_header_line(self.next_line)
self.next_line = self.vcf.readline().rstrip()
self.individuals = self.metadata.individuals
self.logger.info("Setting self.individuals to {0}".format(
self.individuals))
self.header = self.metadata.header
self.vep_header = self.metadata.vep_columns
else:
if not self.fileformat:
raise IOError("Please initialize with a fileformat.")
else:
self.metadata.fileformat = self.fileformat
def add_variant(self,
chrom,
pos,
rs_id,
ref,
alt,
qual,
filt,
info,
form=None,
genotypes=[]):
"""
Add a variant to the parser.
This function is for building a vcf. It takes the relevant parameters
and make a vcf variant in the proper format.
"""
variant_info = [chrom, pos, rs_id, ref, alt, qual, filt, info]
if form:
variant_info.append(form)
for individual in genotypes:
variant_info.append(individual)
variant_line = '\t'.join(variant_info)
variant = format_variant(line=variant_line,
header_parser=self.metadata,
check_info=self.check_info)
if not (self.split_variants and len(variant['ALT'].split(',')) > 1):
self.variants.append(variant)
# If multiple alternative and split_variants we must split the variant
else:
for splitted_variant in split_variants(
variant_dict=variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
self.variants.append(splitted_variant)
def __iter__(self):
if not self.metadata.fileformat:
raise SyntaxError("Vcf must have fileformat defined")
if self.vcf:
# We need to treat the first case as an exception
if self.beginning:
variants = []
if self.next_line:
first_variant = format_variant(line=self.next_line,
header_parser=self.metadata,
check_info=self.check_info)
if not (self.split_variants
and len(first_variant['ALT'].split(',')) > 1):
variants.append(first_variant)
else:
for splitted_variant in split_variants(
variant_dict=first_variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
variants.append(splitted_variant)
for variant in variants:
yield variant
self.beginning = False
for line in self.vcf:
line = line.rstrip()
# These are the variant(s) found in one line of the vcf
# If there are multiple alternatives and self.split_variants
# There can be more than one variant in one line
variants = []
if not line.startswith('#') and len(line.split('\t')) >= 8:
variant = format_variant(line=line,
header_parser=self.metadata,
check_info=self.check_info)
if not (self.split_variants
and len(variant['ALT'].split(',')) > 1):
variants.append(variant)
else:
for splitted_variant in split_variants(
variant_dict=variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
variants.append(splitted_variant)
for variant in variants:
yield variant
else:
for variant in self.variants:
yield variant
def __repr__(self):
return "Parser(infile={0},fsock={1},split_variants={2})".format(
self.infile, self.fsock, self.split_variants)
def __init__(self, infile=None, fsock=None, split_variants=False,
check_info=False, allele_symbol='0', fileformat = None):
super(VCFParser, self).__init__()
self.logger = logging.getLogger(__name__)
self.vcf = None
self.logger.debug("Set self.vcf to:{0}".format(self.vcf))
self.beginning = True
self.infile = infile
self.fsock = fsock
self.split_variants = split_variants
self.logger.info("Split variants = {0}".format(self.split_variants))
self.fileformat = fileformat
self.check_info = check_info
self.logger.info("check info = {0}".format(self.check_info))
self.allele_symbol = allele_symbol
self.logger.info("Allele symbol = {0}".format(self.allele_symbol))
self.logger.info("Initializing HeaderParser")
self.metadata = HeaderParser()
# These are the individuals described in the header
self.individuals = []
# This is the header line of the vcf
self.header = []
# If there are no file or stream the user can add variants manually.
# These will be added to self.variants
self.variants = []
if (fsock or infile):
if fsock:
if not infile and hasattr(fsock, 'name'):
self.logger.info("Reading vcf form stdin")
if sys.version_info < (3, 0):
self.logger.info("Using codecs to read stdin")
sys.stdin = getreader('utf-8')(fsock)
self.vcf = sys.stdin
else:
self.logger.info("Reading vcf form file {0}".format(infile))
file_name, file_extension = os.path.splitext(infile)
if file_extension == '.gz':
self.logger.debug("Vcf is zipped")
self.vcf = getreader('utf-8')(gzip.open(infile), errors='replace')
elif file_extension == '.vcf':
self.vcf = open(infile, mode='r', encoding='utf-8', errors='replace')
else:
raise IOError("File is not in a supported format!\n"
" Or use correct ending(.vcf or .vcf.gz)")
self.logger.debug("Reading first line.")
self.next_line = self.vcf.readline().rstrip()
self.current_line = self.next_line
# First line is allways a metadata line
if not self.next_line.startswith('#'):
raise IOError("VCF files allways have to start with a metadata line.")
self.metadata.parse_meta_data(self.next_line)
# Parse the metadata lines
while self.next_line.startswith('#'):
if self.next_line.startswith('##'):
self.metadata.parse_meta_data(self.next_line)
elif self.next_line.startswith('#'):
self.metadata.parse_header_line(self.next_line)
self.next_line = self.vcf.readline().rstrip()
self.individuals = self.metadata.individuals
self.logger.info("Setting self.individuals to {0}".format(
self.individuals
))
self.header = self.metadata.header
self.vep_header = self.metadata.vep_columns
else:
if not self.fileformat:
raise IOError("Please initialize with a fileformat.")
else:
self.metadata.fileformat = self.fileformat
class VCFParser(object):
"""docstring for VCFParser"""
def __init__(self, infile=None, fsock=None, split_variants=False,
check_info=False, allele_symbol='0', fileformat = None):
super(VCFParser, self).__init__()
self.logger = logging.getLogger(__name__)
self.vcf = None
self.logger.debug("Set self.vcf to:{0}".format(self.vcf))
self.beginning = True
self.infile = infile
self.fsock = fsock
self.split_variants = split_variants
self.logger.info("Split variants = {0}".format(self.split_variants))
self.fileformat = fileformat
self.check_info = check_info
self.logger.info("check info = {0}".format(self.check_info))
self.allele_symbol = allele_symbol
self.logger.info("Allele symbol = {0}".format(self.allele_symbol))
self.logger.info("Initializing HeaderParser")
self.metadata = HeaderParser()
# These are the individuals described in the header
self.individuals = []
# This is the header line of the vcf
self.header = []
# If there are no file or stream the user can add variants manually.
# These will be added to self.variants
self.variants = []
if (fsock or infile):
if fsock:
if not infile and hasattr(fsock, 'name'):
self.logger.info("Reading vcf form stdin")
if sys.version_info < (3, 0):
self.logger.info("Using codecs to read stdin")
sys.stdin = getreader('utf-8')(fsock)
self.vcf = sys.stdin
else:
self.logger.info("Reading vcf form file {0}".format(infile))
file_name, file_extension = os.path.splitext(infile)
if file_extension == '.gz':
self.logger.debug("Vcf is zipped")
self.vcf = getreader('utf-8')(gzip.open(infile), errors='replace')
elif file_extension == '.vcf':
self.vcf = open(infile, mode='r', encoding='utf-8', errors='replace')
else:
raise IOError("File is not in a supported format!\n"
" Or use correct ending(.vcf or .vcf.gz)")
self.logger.debug("Reading first line.")
self.next_line = self.vcf.readline().rstrip()
self.current_line = self.next_line
# First line is allways a metadata line
if not self.next_line.startswith('#'):
raise IOError("VCF files allways have to start with a metadata line.")
self.metadata.parse_meta_data(self.next_line)
# Parse the metadata lines
while self.next_line.startswith('#'):
if self.next_line.startswith('##'):
self.metadata.parse_meta_data(self.next_line)
elif self.next_line.startswith('#'):
self.metadata.parse_header_line(self.next_line)
self.next_line = self.vcf.readline().rstrip()
self.individuals = self.metadata.individuals
self.logger.info("Setting self.individuals to {0}".format(
self.individuals
))
self.header = self.metadata.header
self.vep_header = self.metadata.vep_columns
else:
if not self.fileformat:
raise IOError("Please initialize with a fileformat.")
else:
self.metadata.fileformat = self.fileformat
def add_variant(self, chrom, pos, rs_id, ref, alt, qual, filt, info, form=None, genotypes=[]):
"""
Add a variant to the parser.
This function is for building a vcf. It takes the relevant parameters
and make a vcf variant in the proper format.
"""
variant_info = [chrom, pos, rs_id, ref, alt, qual, filt, info]
if form:
variant_info.append(form)
for individual in genotypes:
variant_info.append(individual)
variant_line = '\t'.join(variant_info)
variant = format_variant(
line = variant_line,
header_parser = self.metadata,
check_info = self.check_info
)
if not (self.split_variants and len(variant['ALT'].split(',')) > 1):
self.variants.append(variant)
# If multiple alternative and split_variants we must split the variant
else:
for splitted_variant in split_variants(
variant_dict=variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
self.variants.append(splitted_variant)
def __iter__(self):
if not self.metadata.fileformat:
raise SyntaxError("Vcf must have fileformat defined")
if self.vcf:
# We need to treat the first case as an exception
if self.beginning:
variants = []
first_variant = format_variant(
line = self.next_line,
header_parser = self.metadata,
check_info = self.check_info
)
if not (self.split_variants and len(first_variant['ALT'].split(',')) > 1):
variants.append(first_variant)
else:
for splitted_variant in split_variants(
variant_dict=first_variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
variants.append(splitted_variant)
for variant in variants:
yield variant
self.beginning = False
for line in self.vcf:
line = line.rstrip()
# These are the variant(s) found in one line of the vcf
# If there are multiple alternatives and self.split_variants
# There can be more than one variant in one line
variants = []
if not line.startswith('#') and len(line.split('\t')) >= 8:
variant = format_variant(
line = line,
header_parser = self.metadata,
check_info = self.check_info
)
if not (self.split_variants and len(variant['ALT'].split(',')) > 1):
variants.append(variant)
else:
for splitted_variant in split_variants(
variant_dict=variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
variants.append(splitted_variant)
for variant in variants:
yield variant
else:
for variant in self.variants:
yield variant
def __repr__(self):
return "Parser(infile={0},fsock={1},split_variants={2})".format(
self.infile, self.fsock, self.split_variants
)
