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.
1 maintainer
Release files for pdbio 0.4.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pdbio-0.4.2.tar.gz | 12.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pdbio-0.4.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 28.0 kB
Release files / pdbio-0.4.2.tar.gz
| Download URL | pdbio-0.4.2.tar.gz |
|---|---|
| Size | 12.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.2.0 requests-toolbelt/0.9.1 tqdm/4.41.1 CPython/3.8.0
|
Release files / pdbio-0.4.2-py3-none-any.whl
| Download URL | pdbio-0.4.2-py3-none-any.whl |
|---|---|
| Size | 16.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.2.0 requests-toolbelt/0.9.1 tqdm/4.41.1 CPython/3.8.0
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