https://github.com/kpj/gene_map
Tool for converting between various gene ids
https://github.com/kpj/gene_map
conversion gene id python uniprot
Last synced: 26 days ago
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Tool for converting between various gene ids
- Host: GitHub
- URL: https://github.com/kpj/gene_map
- Owner: kpj
- Created: 2017-12-12T16:27:21.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-10-15T09:55:23.000Z (over 5 years ago)
- Last Synced: 2025-04-28T14:21:33.368Z (26 days ago)
- Topics: conversion, gene, id, python, uniprot
- Language: Python
- Size: 38.1 KB
- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# gene_map
[](https://pypi.python.org/pypi/gene_map) [](https://travis-ci.org/kpj/gene_map) [](https://codecov.io/gh/kpj/gene_map)
Tool for converting between various gene ids.
## Installation
```bash
$ pip install gene_map
```
## Usage
```bash
$ gene_map --help
Usage: gene_map [OPTIONS]
Map gene ids between various formats.
Options:
-i, --input TEXT If it exists, treated as file with
whitespace-separated gene ids. Otherwise
treated as a gene id itself. [required]
--from TEXT Source ID type. [required]
--to TEXT Target ID type. [required]
-o, --output FILENAME CSV-file to save result to.
--organism [ARATH_3702|CAEEL_6239|CHICK_9031|DANRE_7955|DICDI_44689|DROME_7227|ECOLI_83333|HUMAN_9606|MOUSE_10090|RAT_10116|SCHPO_284812|YEAST_559292]
Organism to convert IDs in.
--cache-dir DIRECTORY Folder to store ID-databases in.
-q, --quiet Suppress logging of mapping-statistics.
--force-download Force download of mapping-database.
--help Show this message and exit.
```
## Getting started
### Commandline usage
Inputs can be either gene ids or files containing whitespace-separated gene ids:
```bash
$ cat mygenes.txt
P63244 P08246
P68871
$ gene_map \
-i P35222 -i InvalidID -i mygenes.txt -i P04637 \
--from ACC --to Gene_Name \
-o gene_mapping.csv
Mapped 5/6 genes.
$ cat gene_mapping.csv
ID_from,ID_to
P04637,TP53
P08246,ELANE
P35222,CTNNB1
P63244,RACK1
P68871,HBB
```
It is also possible to simply try to convert all given inputs without knowing their ID type, by using `--from auto`:
```bash
$ gene_map \
-i P35222 \
-i TP53 \
-i '9606.ENSP00000306407' \
--from auto \
--to GeneID
Mapped 3/3 genes.
ID_from,ID_to
9606.ENSP00000306407,79007
P35222,1499
TP53,7157
```
Attention: if an ID is valid for multiple types, unintended side-effects may occur.
Furthermore, all IDs are treated as strings.
### API usage
```python
>>> from gene_map import GeneMapper
>>> stringdb_ids = ['9606.ENSP00000306407', '9606.ENSP00000337461']
>>> gm = GeneMapper() # defaults to HUMAN_9606
>>> gm.query(stringdb_ids, source_id_type='STRING', target_id_type='GeneID')
# ID_from ID_to
#0 9606.ENSP00000306407 79007
#1 9606.ENSP00000337461 90529
```