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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

Recently I got to know mygene, a python wrapper for the 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 > output.txt
or python input.txt > output.txt  where input.txt contains one gene name in each line. pretty neat!

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