[python] Uniprot ID to Gene name

Question: [python] Uniprot ID to Gene name

Hi, I've got a huge list of Uniprot IDs and I want to get the matching gene names. Do you know how to do that in python ? (I'm currently searching with Biopython...) Thanks !

Yo.

uniprot biopython python

created 2.0 years ago by Yo_O 80•3

See related post here: http://biostar.stackexchange.com/questions/22/gene-id-conversion-tool/8107#8107

2 answers

Perhaps sth like this:

for record in SwissProt.parse(open('uniprot_sprot.dat')):
  accessions = record.accessions
  gene_name = record.gene_name

Chris

created 2.0 years ago by Chris 1,490•2•9

It's a good beginning I think. But my input file is like this : "Uniprot_ID--->position", one per line. So I just want to translate Uniprot_ID to Gene_name in output. Does anything exist yet ? Thx a lot !

Well, my code snippet was rather meant as an inspiration of how to access the uniprot_id and corresponding gene_name from swissprot. Once you have that mapping (e.g. as a dictionary) it should be easy to do the mapping from that to your problem setting.

Yep. I got what I wanted with this :

url = 'http://www.uniprot.org/mapping/'

query=uniprot_id params = {'from':'ACC','to':'ENSEMBL_ID','format':'tab','query':query} data = urllib.urlencode(params) request = urllib2.Request(url, data) response = urllib2.urlopen(request) page = response.read(200000)

Then I've got an homemade dictionary id_Ensembl <-> geneName

Thanks a lot for your answers guys !

Yo.

Oups, I don't know how to paste code here...if an admin can edit it..thanks

You can do this using the retrieve function at www.uniprot.org (4th tab element in the top bar)

Upload your list of ID's.

Look for the small blue UniProtKB (number of retrieved) entries link. Click this. Then use the customize display to select only gene names. Then click download as tab.

Ok, not very pythonic, but a few http calls from python would work.

created 2.0 years ago by Jerven 470•1•4