def accessions(args):
if len(args) == 0:
for it in sys.stdin:
yield it.strip()
else:
for fn in args:
for it in open(fn):
yield it.strip()
gtc = GlyTouCan()
allmotifs = dict()
for acc, label, redend in gtc.allmotifs():
allmotifs[acc] = dict(label=label, redend=redend)
current = set()
for gtcacc in accessions(sys.argv[1:]):
start = time.time()
g = w.get(gtcacc)
newgly = False
if not g:
newgly = True
g = Glycan(accession=gtcacc)
g.delete('wurcs')
g.delete('glycoct')
#!/bin/env python27
import sys
from getwiki import GlycoMotifWiki, GlyTouCanMotif
w = GlycoMotifWiki()
import findpygly
from pygly.GlycanResource import GlyTouCan
gtc = GlyTouCan(usecache=False)
current = set()
for m, l, re in sorted(gtc.allmotifs()):
motif = GlyTouCanMotif(accession=m,
prefname=l,
name=l,
redend=re,
wurcs=gtccache.gtc2wurcs(m),
glycoct=gtccache.gtc2glycoct(m))
if w.update(motif):
print >> sys.stderr, m
current.add(m)
for m in w.itermotif(collection=GlyTouCanMotif):
if m.get('accession') not in current:
print >> sys.stderr, "Deleting:", m.get('pagename')
w.delete(m.get('pagename'))