import xml.dom.minidom as minidom
def getPFamAnnotationByAcc(acc):
res_list = []
slurpp = pycurl.Curl()
slurpp.setopt(pycurl.URL, "http://pfam.sbc.su.se:43210/protein/%s"%acc)
slurpp.setopt(pycurl.POSTFIELDS, "output=xml")
file = open("tmp.xml", "w")
slurpp.setopt(pycurl.FILE, file)
slurpp.perform()
file.close()
#parse the PFam xml file searching for matches
dom = minidom.parse('tmp.xml')
for m in dom.getElementsByTagName('match'):
atts = m.attributes.items()
for l in m.getElementsByTagName('location'):
for t in l.attributes.items():
atts.append(t)
res_list.append(atts)
return res_list
Showing posts with label xml pfam uniprot python pycurl post method. Show all posts
Showing posts with label xml pfam uniprot python pycurl post method. Show all posts
Saturday, March 28, 2009
Access PFAM domains from UniProt accessions using python
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