Source code for petlx.bio.vcf

# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division


import petl as etl
from petl.util.base import Table


[docs]def fromvcf(filename, chrom=None, start=None, stop=None, samples=True): """ Returns a table providing access to data from a variant call file (VCF). E.g.:: >>> import petl as etl >>> # activate bio extensions ... import petlx.bio >>> table1 = etl.fromvcf('fixture/sample.vcf') >>> table1.look(truncate=20) +-------+---------+-------------+-----+--------+------+---------+----------------------+----------------------+----------------------+----------------------+ | CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | NA00001 | NA00002 | NA00003 | +=======+=========+=============+=====+========+======+=========+======================+======================+======================+======================+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | Call(sample=NA00001, | Call(sample=NA00002, | Call(sample=NA00003, | +-------+---------+-------------+-----+--------+------+---------+----------------------+----------------------+----------------------+----------------------+ | '19' | 112 | None | 'A' | [G] | 10 | None | {} | Call(sample=NA00001, | Call(sample=NA00002, | Call(sample=NA00003, | +-------+---------+-------------+-----+--------+------+---------+----------------------+----------------------+----------------------+----------------------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | {'DP': 14, 'H2': Tru | Call(sample=NA00001, | Call(sample=NA00002, | Call(sample=NA00003, | +-------+---------+-------------+-----+--------+------+---------+----------------------+----------------------+----------------------+----------------------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | {'DP': 11, 'NS': 3, | Call(sample=NA00001, | Call(sample=NA00002, | Call(sample=NA00003, | +-------+---------+-------------+-----+--------+------+---------+----------------------+----------------------+----------------------+----------------------+ | '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | {'DP': 10, 'AA': 'T' | Call(sample=NA00001, | Call(sample=NA00002, | Call(sample=NA00003, | +-------+---------+-------------+-----+--------+------+---------+----------------------+----------------------+----------------------+----------------------+ ... """ return VCFView(filename, chrom=chrom, start=start, stop=stop, samples=samples)
etl.fromvcf = fromvcf VCF_HEADER = ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO') class VCFView(Table): def __init__(self, filename, chrom=None, start=None, stop=None, samples=True): self.filename = filename self.chrom = chrom self.start = start self.stop = stop self.samples = samples def __iter__(self): import vcf as pyvcf reader = pyvcf.Reader(filename=self.filename) # determine header if isinstance(self.samples, (list, tuple)): # specific samples requested yield VCF_HEADER + tuple(self.samples) elif self.samples: # all samples yield VCF_HEADER + tuple(reader.samples) else: # no samples yield VCF_HEADER # fetch region? if None not in [self.chrom, self.start]: it = reader.fetch(self.chrom, self.start, self.end) else: it = reader # yield data for variant in it: out = tuple(getattr(variant, f) for f in VCF_HEADER) if isinstance(self.samples, (list, tuple)): # specific samples requested out += tuple(variant.genotype(s) for s in self.samples) elif self.samples: # all samples out += tuple(variant.samples) yield out
[docs]def vcfunpackinfo(table, *keys): """ Unpack the INFO field into separate fields. E.g.:: >>> import petl as etl >>> # activate bio extensions ... import petlx.bio >>> table1 = ( ... etl ... .fromvcf('fixture/sample.vcf', samples=None) ... .vcfunpackinfo() ... ) >>> table1 +-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+ | CHROM | POS | ID | REF | ALT | QUAL | FILTER | AA | AC | AF | AN | DB | DP | H2 | NS | +=======+=========+=============+=====+========+======+=========+======+======+================+======+======+======+======+======+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | None | None | None | None | None | None | None | None | +-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+ | '19' | 112 | None | 'A' | [G] | 10 | None | None | None | None | None | None | None | None | None | +-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+ | '20' | 14370 | 'rs6054257' | 'G' | [A] | 29 | [] | None | None | [0.5] | None | True | 14 | True | 3 | +-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+ | '20' | 17330 | None | 'T' | [A] | 3 | ['q10'] | None | None | [0.017] | None | None | 11 | None | 3 | +-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+ | '20' | 1110696 | 'rs6040355' | 'A' | [G, T] | 67 | [] | 'T' | None | [0.333, 0.667] | None | True | 10 | None | 2 | +-------+---------+-------------+-----+--------+------+---------+------+------+----------------+------+------+------+------+------+ ... """ result = etl.unpackdict(table, 'INFO', keys=keys) return result
etl.vcfunpackinfo = vcfunpackinfo Table.vcfunpackinfo = vcfunpackinfo
[docs]def vcfmeltsamples(table, *samples): """ Melt the samples columns. E.g.:: >>> import petl as etl >>> # activate bio extensions ... import petlx.bio >>> table1 = ( ... etl ... .fromvcf('fixture/sample.vcf') ... .vcfmeltsamples() ... ) >>> table1 +-------+-----+------+-----+-----+------+--------+------+-----------+-----------------------------------------------------+ | CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | SAMPLE | CALL | +=======+=====+======+=====+=====+======+========+======+===========+=====================================================+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | 'NA00001' | Call(sample=NA00001, CallData(GT=0|0, HQ=[10, 10])) | +-------+-----+------+-----+-----+------+--------+------+-----------+-----------------------------------------------------+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | 'NA00002' | Call(sample=NA00002, CallData(GT=0|0, HQ=[10, 10])) | +-------+-----+------+-----+-----+------+--------+------+-----------+-----------------------------------------------------+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | 'NA00003' | Call(sample=NA00003, CallData(GT=0/1, HQ=[3, 3])) | +-------+-----+------+-----+-----+------+--------+------+-----------+-----------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | None | {} | 'NA00001' | Call(sample=NA00001, CallData(GT=0|0, HQ=[10, 10])) | +-------+-----+------+-----+-----+------+--------+------+-----------+-----------------------------------------------------+ | '19' | 112 | None | 'A' | [G] | 10 | None | {} | 'NA00002' | Call(sample=NA00002, CallData(GT=0|0, HQ=[10, 10])) | +-------+-----+------+-----+-----+------+--------+------+-----------+-----------------------------------------------------+ ... """ result = etl.melt(table, key=VCF_HEADER, variables=samples, variablefield='SAMPLE', valuefield='CALL') return result
etl.vcfmeltsamples = vcfmeltsamples Table.vcfmeltsamples = vcfmeltsamples
[docs]def vcfunpackcall(table, *keys): """ Unpack the call column. E.g.:: >>> import petl as etl >>> # activate bio extensions ... import petlx.bio >>> table1 = ( ... etl ... .fromvcf('fixture/sample.vcf') ... .vcfmeltsamples() ... .vcfunpackcall() ... ) >>> table1 +-------+-----+------+-----+-----+------+--------+------+-----------+------+------+-------+----------+ | CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | SAMPLE | DP | GQ | GT | HQ | +=======+=====+======+=====+=====+======+========+======+===========+======+======+=======+==========+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | 'NA00001' | None | None | '0|0' | [10, 10] | +-------+-----+------+-----+-----+------+--------+------+-----------+------+------+-------+----------+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | 'NA00002' | None | None | '0|0' | [10, 10] | +-------+-----+------+-----+-----+------+--------+------+-----------+------+------+-------+----------+ | '19' | 111 | None | 'A' | [C] | 9.6 | None | {} | 'NA00003' | None | None | '0/1' | [3, 3] | +-------+-----+------+-----+-----+------+--------+------+-----------+------+------+-------+----------+ | '19' | 112 | None | 'A' | [G] | 10 | None | {} | 'NA00001' | None | None | '0|0' | [10, 10] | +-------+-----+------+-----+-----+------+--------+------+-----------+------+------+-------+----------+ | '19' | 112 | None | 'A' | [G] | 10 | None | {} | 'NA00002' | None | None | '0|0' | [10, 10] | +-------+-----+------+-----+-----+------+--------+------+-----------+------+------+-------+----------+ ... """ result = ( etl.wrap(table) .convert('CALL', lambda v: v.data._asdict()) .unpackdict('CALL', keys=keys) ) return result
etl.vcfunpackcall = vcfunpackcall Table.vcfunpackcall = vcfunpackcall