gene_map
Tool for converting between various gene ids.
Installation
$ pip install gene_mapUsage
$ 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:
$ 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,HBBIt is also possible to simply try to convert all given inputs without knowing their ID type, by using --from auto:
$ 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
TP53,7157Attention: if an ID is valid for multiple types, unintended side-effects may occur. Furthermore, all IDs are treated as strings.
API usage
>>> 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