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[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
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updated by Jerven • Jerven • written by Yo_O • Yo_O

2 answers

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.

• 1 views • link
written by Jerven • Jerven

Perhaps sth like this:

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

Chris

• 0 views • link
written by Chris • Chris

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 !

• 1 views • link
written by Yo_O • Yo_O

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.

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written by Chris • Chris

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.

• 0 views • link
written by Yo_O • Yo_O

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

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written by Yo_O • Yo_O

Can you share the code with us which you said "I canot paste it here " ?

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written by mehmetazizyirik • mehmetazizyirik

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