Creative Commons License
This blog by Tommy Tang is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

My github papge

Wednesday, September 3, 2014

mapping gene ids with mygene

Mapping gene ids is one of the routine jobs for bioinformatics. I was aware of several ways to do it including Biomart.

Update on 10/30/14, a mygene bioconductor package is online http://bioconductor.org/packages/release/bioc/html/mygene.html

Recently I got to know mygene, a python wrapper for the mygene.info services to map gene ids.
I found it very handy to convert gene ids.  see a gist below.

To use it,  cat input.txt | python geneSymbol2Entrez.py > output.txt
or python geneSymbol2Entrez.py input.txt > output.txt  where input.txt contains one gene name in each line. pretty neat!

No comments:

Post a Comment