from getwiki import GPTWiki, Glycan import findpygly from pygly.GlyTouCan import GlyTouCan import os, sys, urllib, string import Bio.SeqIO gtc = GlyTouCan(usecache=True) w = GPTWiki() try: os.mkdir('../glycoct') except OSError: pass for gc in sorted(w.iterglycans(), key=lambda gc: gc.get('accession')): acc = gc.get('accession') topos = map(str.strip, map(str, gc.get('topo'))) for tacc in topos: glycoct = gtc.getseq(tacc, 'glycoct') if not glycoct: gly = gtc.getGlycan(tacc) glycoct = gly.glycoct() f = open('../glycoct/' + acc + '.' + tacc + '.txt', 'w') f.write(glycoct) f.close() print >> sys.stderr, "Dump GlycoCT to %s.%s.txt" % (acc, tacc)
#!/bin/env python27 from getwiki import GPTWiki import re w = GPTWiki() monos = "NHSF" for gly in w.iterglycans(): gsym = gly.get('sym') mcnt = {} for mono in monos: mcnt[mono] = 0 m = re.search(mono + r'(\d+)', gsym) if m: mcnt[mono] = int(m.group(1)) elif mono in gsym: mcnt[mono] = 1 gly.set('nneuac', mcnt['S']) if w.put(gly): print gly.get('id') for pep in w.iterpeptides(): pepname = pep.get('name') pep.set('nox', pepname.count('[Ox]')) if w.put(pep): print pep.get('id')