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
Saturday, March 28, 2009
Access PFAM domains from UniProt accessions using python
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