py1kgp
Utilities for working with 1000 Genomes data
Installation
First make sure you have followed the installation procedure for
pydbsnp. Then install py1kgp
with pip3:
pip3 install py1kgp
or
pip3 install --user py1kgp
For full functionality, you should appropriately set the environment variable
PY1KGP_DIR. For example, you could add this to your .bash_profile:
export PY1KGP_DIR=<path to directory of your choice>
Examples
import py1kgp
py1kgp.Variant('rs10')
py1kgp.Variant(id='rs10')
py1kgp.Variant(7, 92383888)
py1kgp.Variant(chrom=7, pos=92383888)
py1kgp.fast_genotypes(7, 92383888)
py1kgp.fast_genotypes(7, 92383888, samples='NA21142,NA21143,NA21144')
py1kgp.fast_maf(7, 92383888)
py1kgp.slice_vcf(1, 1000000, 2000000)
py1kgp.slice_vcf(1, 1000000, 2000000, samples='NA21142,NA21143,NA21144')
py1kgp.slice_vcf(1, 1000000, 2000000, samples='AFR')
py1kgp.slice_vcf(1, 1000000, 2000000, samples='samples.panel')
1 maintainer
Metadata
1 maintainer
Release files for py1kgp 0.1.2
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| py1kgp-0.1.2.tar.gz | 5.0 kB | Without provenance | Details for py1kgp-0.1.2.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| py1kgp-0.1.2-py3-none-any.whl | Python 3 | none | any | Details for py1kgp-0.1.2-py3-none-any.whl |
Total release size: 10.6 kB
Release files / py1kgp-0.1.2.tar.gz
| Download URL | py1kgp-0.1.2.tar.gz |
|---|---|
| Size | 5.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / py1kgp-0.1.2-py3-none-any.whl
| Download URL | py1kgp-0.1.2-py3-none-any.whl |
|---|---|
| Size | 5.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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twine/4.0.1 CPython/3.9.10
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