Description:

pdbio 0.4.2

pdbio
Pandas-based Data Handler for VCF, BED, and SAM Files

Installation
$ pip install -U pdbio

Python API
Example of API call
from pprint import pprint
from pdbio.vcfdataframe import VcfDataFrame

vcf_path = 'test/example.vcf'
vcfdf = VcfDataFrame(path=vcf_path)

pprint(vcfdf.header) # list of header
pprint(vcfdf.samples) # list of samples
print(vcfdf.df) # VCF dataframe

vcfdf.sort() # sort by CHROM, POS, and the other
print(vcfdf.df) # sorted dataframe

Command-line interface
Example of commands
# Convert VCF data into sorted TSV data
$ pdbio vcf2csv --sort --tsv test/example.vcf

# Convert VCF data into expanded CSV data
$ pdbio vcf2csv --expand-info --expand-samples test/example.vcf

# Sort VCF data by CHROM, POS, and the other
$ pdbio vcfsort test/example.vcf

Run pdbio --help for more information.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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