pdbio 0.4.2
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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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