vcfiterator 0.1-pre4

A package for iterating of .vcf files, parsing it to data structures. Especially useful for converting vcf files to JSON.

Python module for iterating over a VCF file, parsing and generating data structures. Targeted at understanding annotation data, and creating JSON output.

This module is still very much a WIP, but is fully working.

Background

Parsing VCF files into a more machine usable format can be difficult, especially when dealing with INFO fields from annotation software. Most annotation programs use their own custom format. To support parsing such INFO fields, vcfiterator has a plugin system for supporting custom fields.

The main purpose for this module is to be able to parse VCF files and generate usable JSON from it, with no further parsing necessary. It can also be useful for any task where the annotation data needs to be readily available.

Features

It currently supports output from the following annotation software:

1. VEP release 79

2. snpEff

You can easily add support for more software (see BaseInfoProcessor in processors.py). Pull requests are welcome.

It does not yet support tabix indexing or compressed VCF files.

Usage

Simple example showing general usage:

from vcfiterator import VcfIterator
from vcfiterator.processors import VEPInfoProcessor, SnpEffInfoProcessor

v = VcfIterator(path)
v.addInfoProcessor(VEPInfoProcessor)
v.addInfoProcessor(SnpEffInfoProcessor)

# Print all VEP info for all variants
for variant in v.iter():
    alleles = variant['ALT']
    for allele in alleles:
        print allele
        print variant['INFO'][allele]['CSQ']

Example output

In short, it takes a VCF line like the following:

5   179390472   .   C   A   21.77   LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;CSQ=A|55819|NM_018434.5|Transcript|stop_gained&splice_region_variant|1659|1243|415|E/*|Gag/Tag||1||-1|protein_coding|YES||NP_060904.2|||8/9|||NM_018434.5:c.1243G>T|NP_060904.2:p.Glu415Ter||||||||||||||,A|ENSG00000113269|ENST00000519708|Transcript|downstream_gene_variant|||||||1|3511|-1|retained_intron||||||||||||||||||||||||,A|55819|NM_001280801.1|Transcript|intron_variant|||||||1||-1|protein_coding|||NP_001267730.1||||7/7||NM_001280801.1:c.1150+3334G>T|||||||||||||||,A|ENSG00000113269|ENST00000521389|Transcript|stop_gained&splice_region_variant|1659|1243|415|E/*|Gag/Tag||1||-1|protein_coding|YES|CCDS4451.1|ENSP00000430237|||8/9|||ENST00000521389.1:c.1243G>T|ENSP00000430237.1:p.Glu415Ter||||||||||||||,A|ENSG00000113269|ENST00000522208|Transcript|intron_variant|||||||1||-1|protein_coding|||ENSP00000429509||||7/7||ENST00000522208.2:c.1150+3334G>T|||||||||||||||,A|ENSG00000113269|ENST00000521901|Transcript|splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|472||||||1||-1|retained_intron||||||1/2|||ENST00000521901.1:n.472G>T|||||||||||||||,A|ENSG00000249412|ENST00000510240|Transcript|upstream_gene_variant|||||||1|143|1|antisense|YES|||||||||||||||||||||||,A|ENSG00000113269|ENST00000520911|Transcript|splice_region_variant&3_prime_UTR_variant&NMD_transcript_variant|1599||||||1||-1|nonsense_mediated_decay|||ENSP00000430999|||8/9|||ENST00000520911.1:c.*762G>T|||||||||||||||,A|ENSG00000113269|ENST00000261947|Transcript|intron_variant|||||||1||-1|protein_coding||CCDS64340.1|ENSP00000261947||||7/7||ENST00000261947.4:c.1150+3334G>T|||||||||||||||;EFF=stop_gained(HIGH|NONSENSE|Gag/Tag|p.Glu415*/c.1243G>T|419|RNF130|protein_coding|CODING|ENST00000521389|8|1),splice_region_variant(LOW|||c.1243G>T|419|RNF130|protein_coding|CODING|ENST00000521389|8|1),splice_region_variant(LOW|||||RNF130|nonsense_mediated_decay|CODING|ENST00000520911|8|1),splice_region_variant(LOW|||n.472G>T||RNF130|retained_intron|CODING|ENST00000521901|1|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|7|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|4|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|3|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|9|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|6|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|5|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.1243C>A|419|RNF130|protein_coding|CODING|ENST00000521389|8|1),3_prime_UTR_variant(MODIFIER||49801|n.*762G>T||RNF130|nonsense_mediated_decay|CODING|ENST00000520911|8|1),upstream_gene_variant(MODIFIER||143|||CTC-563A5.2|antisense|NON_CODING|ENST00000510240||1),downstream_gene_variant(MODIFIER||3511|||RNF130|retained_intron|CODING|ENST00000519708||1),intron_variant(MODIFIER|||c.1150+3334G>T|419|RNF130|protein_coding|CODING|ENST00000522208|7|1),intron_variant(MODIFIER|||c.1150+3334G>T|384|RNF130|protein_coding|CODING|ENST00000261947|7|1),non_coding_exon_variant(MODIFIER|||n.472G>T||RNF130|retained_intron|CODING|ENST00000521901|1|1) GT:AD:DP:GQ:PL  1/1:0,2:2:6:49,6,0

and turns it into a data structure:

{'ALT': ['A'],
 'CHROM': '5',
 'FILTER': 'LowQual',
 'ID': '.',
 'INFO': {'A': {'AC': '2',
                'AF': '1.0',
                'CSQ': [{'ALLELE_NUM': 1,
                         'Allele': 'A',
                         'Amino_acids': 'E/*',
                         'BIOTYPE': 'protein_coding',
                         'CANONICAL': 'YES',
                         'CDS_position': '1243',
                         'Codons': 'Gag/Tag',
                         'Consequence': 'stop_gained&splice_region_variant',
                         'ENSP': 'NP_060904.2',
                         'EXON': '8/9',
                         'Feature': 'NM_018434.5',
                         'Feature_type': 'Transcript',
                         'Gene': '55819',
                         'HGVSc': 'NM_018434.5:c.1243G>T',
                         'HGVSp': 'NP_060904.2:p.Glu415Ter',
                         'Protein_position': '415',
                         'STRAND': -1,
                         'cDNA_position': '1659'},

                        ....

                        {'ALLELE_NUM': 1,
                         'Allele': 'A',
                         'BIOTYPE': 'protein_coding',
                         'CCDS': 'CCDS64340.1',
                         'Consequence': 'intron_variant',
                         'ENSP': 'ENSP00000261947',
                         'Feature': 'ENST00000261947',
                         'Feature_type': 'Transcript',
                         'Gene': 'ENSG00000113269',
                         'HGVSc': 'ENST00000261947.4:c.1150+3334G>T',
                         'INTRON': '7/7',
                         'STRAND': -1}],
                'EFF': [{'Amino_Acid_Change': 'p.Glu415*/c.1243G>T',
                         'Amino_Acid_length': 419,
                         'Codon_Change': 'Gag/Tag',
                         'Effect': 'stop_gained',
                         'Effect_Impact': 'HIGH',
                         'Exon_Rank': 8,
                         'Functional_Class': 'NONSENSE',
                         'Gene_Coding': 'CODING',
                         'Gene_Name': 'RNF130',
                         'Genotype_Number': 1,
                         'Transcript_BioType': 'protein_coding',
                         'Transcript_ID': 'ENST00000521389'},

                        ....

                        {'Amino_Acid_Change': 'n.472G>T',
                         'Effect': 'non_coding_exon_variant',
                         'Effect_Impact': 'MODIFIER',
                         'Exon_Rank': 1,
                         'Gene_Coding': 'CODING',
                         'Gene_Name': 'RNF130',
                         'Genotype_Number': 1,
                         'Transcript_BioType': 'retained_intron',
                         'Transcript_ID': 'ENST00000521901'}],
                'MLEAC': '2',
                'MLEAF': '1.0'},
          'ALL': {'AN': '2',
                  'DP': '2',
                  'FS': '0.0',
                  'MQ': '60.0',
                  'MQ0': '0',
                  'QD': '10.88'}},
 'POS': 179390472,
 'QUAL': 21.77,
 'REF': 'C',
 'SAMPLES': {'TEST_CHR5': {'AD': [0, 2],
                           'DP': 2,
                           'GQ': 6,
                           'GT': '1/1',
                           'PL': [49, 6, 0]}}}