Does anyone know of a good gene-id conversion tool written in Python. I've come across numerous webtools but I'd like something a little more automated. I have the knowledge/ability to do it myself I was just wondering if there was something already out there. There's no point in re-inventing the wheel each time.
Thanks in advance
Writing a small tool to automate access to the website/service is pretty simple. Here's a method I wrote for the UniProt ID mapping service:
import urllib
import urllib2
def uniprot_mapping(fromtype, totype, identifier):
base = 'http://www.uniprot.org'
tool = 'mapping'
params = {'from':fromtype,
'to':totype,
'format':'tab',
'query':identifier,
}
data = urllib.urlencode(params)
url = base+'/'+tool+'?'+data
response = urllib2.urlopen(url)
return response.read()
It's not extensively tested, but should work. You can find a list of fromtypes and totypes here: http://www.uniprot.org/faq/28#id_mapping_examples
•
written
by
Simon Cockell
I should note that DAVIS has an API: http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html but it doesn't seem to cover their ID mapping service.
Oh and also, Tim Yates has written a Groovy version of my code, above: http://gist.github.com/330312
I should note that DAVID has an API: http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html but it doesn't seem to cover their ID mapping service.
Check out the python library for mygene.info. For example:
In [1]: import mygene
In [2]: mg = mygene.MyGeneInfo()
In [3]: mg.getgene(1017)
Out[3]:
{'_id': '1017',
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'symbol': 'CDK2',
'taxid': 9606}
In [4]: mg.query('cdk2', size=2)
Out[4]:
{'hits': [{'_id': '1017',
'_score': 373.24667,
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'symbol': 'CDK2',
'taxid': 9606},
{'_id': '12566',
'_score': 353.90176,
'entrezgene': 12566,
'name': 'cyclin-dependent kinase 2',
'symbol': 'Cdk2',
'taxid': 10090}],
'max_score': 373.24667,
'took': 10,
'total': 28}
A few nice features of mygene.info
More information in this publication and on these blog posts.
In case anyone comes by this later I've made a simple python module for doing this sort of converting. You can find it on GitHub: http://github.com/JudoWill/IDConverter
Feel free make comments and provide suggestions.
the link is broken:/ UPDATE: okay, now I see the date of this post.
You could automate the access to the website with Python ;-)
Have you come across bioDBnet?
•
written
by
Prakki Rama
Log in to answer this question.
Which Ids do you want to convert, exactly? I think there is not a single service that can convert between all the most used ids for genes, even biomart and uniprot lack some databases. Look at this question.