Tutorial on MetaData

Advanced tutorial on vcf parser module showing available methods for parsing metadata.

First import VcfParser module and instantiate an vcf object by passing vcf file as an argument.

Initial setup:

>>> from vcfparser import VcfParser
>>> vcf_obj = VcfParser('input_test.vcf')

We can also pass gzipped vcf file as an argument.

>>> vcf_obj = VcfParser('input_test.vcf.gz')

VcfParser module has two main methods:

  • parse_metadata: It contains methods for extracting information related to the metadata header.
  • parse_records: It contains methods for retrieving the record values from the vcf file.

Parsing VCF metadata:

To parse the metadata information we can call parse_metadata():

>>> # pass the VCF object to the 'parse_metadata()' function
>>> metainfo = vcf_obj.parse_metadata()

  • Metainfo provides several attributes and objects that helps in extracting specific metadata information.
  • These informations are reported as a list or dictionary.

To list all the available attributes within metainfo do:

>>> metainfo.__dir__()
['header_file', 'infos_', 'filters_', 'contig', 'format_', 'alt_', 'other_lines', 'fileformat', 'reference', 'sample_names', 'is_gvcf', 'gvcf_blocks', 'record_keys', 'VCFspec', 'gatk_commands', 'raw_meta_data', '_format_pattern', '_meta_pattern', 'sample_with_pos', '__module__', '__doc__', '__init__', '_parse_gvcf_block', '_parse_gatk_commands', 'parse_lines', '__dict__', '__weakref__', '__repr__', '__hash__', '__str__', '__getattribute__', '__setattr__', '__delattr__', '__lt__', '__le__', '__eq__', '__ne__', '__gt__', '__ge__', '__new__', '__reduce_ex__', '__reduce__', '__subclasshook__', '__init_subclass__', '__format__', '__sizeof__', '__dir__', '__class__']
>>> # or
>>> dir(metainfo)
['VCFspec', '__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_format_pattern', '_meta_pattern', '_parse_gatk_commands', '_parse_gvcf_block', 'alt_', 'contig', 'fileformat', 'filters_', 'format_', 'gatk_commands', 'gvcf_blocks', 'header_file', 'infos_', 'is_gvcf', 'other_lines', 'parse_lines', 'raw_meta_data', 'record_keys', 'reference', 'sample_names', 'sample_with_pos', 'testA']

To call the specific objects and attributes do:

>>> metainfo.VCFspec
[{'fileformat': 'VCFv4.2'}, {'GVCF': True}]


>>> metainfo.infos_
[{'ID': 'AF', 'Number': 'A', 'Type': 'Float', 'Description': 'Allele Frequency, for each ALT allele, in the same order as listed'}, {'ID': 'BaseQRankSum', 'Number': '1', 'Type': 'Float', 'Description': 'Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities'}, {'ID': 'ClippingRankSum', 'Number': '1', 'Type': 'Float', 'Description': 'Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases'}, {'ID': 'DP', 'Number': '1', 'Type': 'Integer', 'Description': 'Approximate read depth; some reads may have been filtered'},
{'ID': 'DS', 'Number': '0', 'Type': 'Flag', 'Description': 'Were any of the samples downsampled?'}, {'ID': 'END', 'Number': '1', 'Type': 'Integer', 'Description': 'Stop position of the interval'}, {'ID': 'ExcessHet', 'Number': '1', 'Type': 'Float', 'Description': 'Phred-scaled p-value for exact test of excess heterozygosity'}, {'ID': 'FS', 'Number': '1', 'Type': 'Float', 'Description': "Phred-scaled p-value using Fisher's exact test to detect strand bias"}, {'ID': 'HaplotypeScore', 'Number': '1', 'Type': 'Float', 'Description': 'Consistency of the site with at most two segregating haplotypes'}, {'ID': 'InbreedingCoeff', 'Number': '1', 'Type': 'Float', 'Description': 'Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation'}, {'ID': 'MLEAC', 'Number': 'A', 'Type': 'Integer', 'Description': 'Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed'}, {'ID': 'MLEAF', 'Number': 'A', 'Type': 'Float', 'Description': 'Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed'}, {'ID': 'MQ', 'Number': '1', 'Type': 'Float', 'Description': 'RMS Mapping Quality'}, {'ID': 'MQRankSum', 'Number': '1', 'Type': 'Float', 'Description': 'Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities'}, {'ID': 'QD', 'Number': '1', 'Type': 'Float', 'Description': 'Variant Confidence/Quality by Depth'}, {'ID': 'RAW_MQ', 'Number': '1', 'Type': 'Float', 'Description': 'Raw data for RMS Mapping
Quality'}, {'ID': 'ReadPosRankSum', 'Number': '1', 'Type': 'Float', 'Description': 'Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias'}, {'ID': 'SOR', 'Number': '1', 'Type': 'Float', 'Description': 'Symmetric Odds Ratio of 2x2 contingency table to detect strand bias'}, {'ID': 'set', 'Number': '1', 'Type': 'String', 'Description': 'Source VCF for the merged record in CombineVariants'}, {'ID': 'SF', 'Number': '.', 'Type': 'String', 'Description': 'Source File (index to sourceFiles, f when filtered)'}, {'ID': 'AC', 'Number': '.',
'Type': 'Integer', 'Description': 'Allele count in genotypes'}, {'ID': 'AN', 'Number': '1', 'Type': 'Integer', 'Description': 'Total number of alleles in called genotypes'}, {'ID': 'TS', 'Type': 'Test', 'Description': 'Allele count in genotypes'}]


>>> metainfo.record_keys
['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'ms01e', 'ms02g', 'ms03g', 'ms04h', 'MA611', 'MA605', 'MA622']