Set of tools for working with vcf files and variants.
Thanks to pyvcf for code base in header parser.
def get_variant_dict(variant_line, header_line):
"""Parse a variant line
Split a variant line and map the fields on the header columns
Args:
variant_line (str): A vcf variant line
header_line (list): A list with the header columns
Returns:
variant_dict (dict): A variant dictionary
"""def get_info_dict(info_line):
"""Parse a info field of a variant
Make a dictionary from the info field of a vcf variant.
Keys are the info keys and values are the raw strings from the vcf
If the field only have a key (no value), value of infodict is True.
Args:
info_line (str): The info field of a vcf variant
Returns:
info_dict (dict): A INFO dictionary
"""def get_variant_id(variant_dict):
"""Build a variant id
The variant id is a string made of CHROM_POS_REF_ALT
Args:
variant_dict (dict): A variant dictionary
Returns:
variant_id (str)
"""def get_vep_info(vep_string, vep_header):
"""Make the vep annotations into a dictionaries
A vep dictionary will have the vep column names as keys and
the vep annotations as values.
The dictionaries are stored in a list
Args:
vep_list (string): A string with the CSQ annotation
vep_header (list): A list with the vep header
allele (str): The allele that is annotated
Return:
vep_annotations (list): A list of vep dicts
"""def replace_vcf_info(keyword, annotation, variant_line=None, variant_dict=None):
"""Replace the information of a info field of a vcf variant line or a
variant dict.
Arguments:
variant_line (str): A vcf formatted variant line
variant_dict (dict): A variant dictionary
keyword (str): The info field key
annotation (str): If the annotation is a key, value pair
this is the string that represents the value
Returns:
variant_line (str): A annotated variant linedef add_vcf_info(keyword, variant_line=None, variant_dict=None, annotation=None):
"""
Add information to the info field of a vcf variant line.
Arguments:
keyword (str): The info field key
variant_line (str): A vcf formatted variant line
annotation (str): If the annotation is a key, value pair
this is the string that represents the value
Returns:
fixed_variant : str if variant line, or dict if variant_dict
"""class Genotype(object):
"""Holds information about a vcf genotype
These objects try to collect the relevant information about genotype
calls in the vcf format.
Attributes:
allele_1 = '.'
allele_2 = '.'
genotype = './.'
heterozygote = False
allele_depth = False
homo_alt = False
homo_ref = False
has_variant = False
genotyped = False
phased = False
depth_of_coverage = 0
quality_depth = 0
genotype_quality = 0
ref_depth = 0
alt_depth = 0
quality_depth = ref_depth + alt_depth
phred_likelihoods = []
"""class HeaderParser(object):
"""Class for holding and manipulating vcf headers
Attributes:
info_dict=OrderedDict()
extra_info = {}
filter_lines=[]
filter_dict=OrderedDict()
contig_lines=[]
contig_dict=OrderedDict()
format_lines=[]
format_dict=OrderedDict()
alt_lines=[]
alt_dict=OrderedDict()
other_lines=[]
other_dict=OrderedDict()
header=['CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO']
header_keys={'info' : ['ID', 'Number', 'Type', 'Description'],
'form' : ['ID', 'Number', 'Type', 'Description'],
'filt' : ['ID', 'Description'],
'alt' : ['ID', 'Description'],
'contig' : ['ID', 'length']}
fileformat = None
filedate = None
reference = None
phasing = None
source = None
line_counter = 0
individuals = []
vep_columns = []
info_pattern
filter_pattern
contig_pattern
format_pattern
alt_pattern
meta_pattern
Methods:
parse_meta_data(line)
parse_header_line(line)
add_fileformat(fileformat)
print_header(): Return a list with the header lines
add_meta_linekey, value)
add_info(info_id, number, entry_type, description)
add_filter(filter_id, description)
add_format(format_id, number, entry_type, description)
add_alt(alt_id, description)
add_contig(contig_id, length)
add_version_tracking(info_id, version, date, command_line='')
"""