Pandas-based Data Handler for VCF, BED, and SAM Files
Project description
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.
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