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')