Map gene ids using uniprot's website.
Project description
Tool for converting between various gene ids.
Installation
$ pip install gene_map
Usage
$ 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 TEXT CSV-file to save result to.
--help Show this message and exit.
Getting started
Inputs can be either gene ids or files containing whitespace-separated gene ids:
$ cat mygenes.txt
P63244 P08246
P68871
$ gene_map -i P35222 -i InvalidID -i mygenes.txt -i P04637 --from ACC --to Gene_Name
ID_from,ID_to
P35222,CTNNB1
InvalidID,
P63244,RACK1
P08246,ELANE
P68871,HBB
P04637,TP53
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gene_map-0.2.1.tar.gz
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