monosdb = {}
f = open(sys.argv[1], 'r')
for line in f:
k, v = line.split()
monosdb[k] = v
for g in w.iterglycan():
acc = g.get('accession')
monodbids = set()
glycan = g.getGlycan()
if not glycan:
continue
for m in glycan.all_nodes():
try:
glycoctsym = glycoctformat.mtoStr(m)
except KeyError:
continue
try:
monodbids.add(monosdb[glycoctsym])
except KeyError:
continue
g.delete_annotations(source="EdwardsLab",
property="MonosaccharideDB",
type="CrossReference")
g.set_annotation(value=monodbids,
property="MonosaccharideDB",
source="EdwardsLab",
type="CrossReference")
if w.put(g):
print acc
#!/bin/env python27
import sys
from getwiki import GlycanData
w = GlycanData()
import findpygly
from pygly.CompositionTable import PermethylCompositionTable
from pygly.GlycanFormatter import GlycoCTFormat
pctable = PermethylCompositionTable()
glycoctformat = GlycoCTFormat()
for g in w.iterglycan():
glycan = g.getGlycan()
if not glycan:
continue
for m in glycan.all_nodes():
try:
eltcomp = m.composition(pctable)
except KeyError:
print g.get('accession'), glycoctformat.mtoStr(m)
for m in glycan.all_nodes(undet_subst=True):
node_count += 1
if node_count == 0:
continue
if glycan.has_root() and node_count != 1:
continue
special_node_count_one = False
if glycan.has_root() and node_count == 1:
r = glycan.root()
floating_subst = []
for sl in r.substituent_links():
try:
glycoctsym = glycoctformat.mtoStr(sl.child())
except KeyError:
continue
if sl.parent_pos() != None:
continue
if glycoctsym in basecomp:
sub = sl.child()
sub.set_connected(False)
r.remove_substituent_link(sl)
floating_subst.append(sub)
glycan.set_root(None)
glycan.set_undetermined([r]+floating_subst)
node_count = len(floating_subst)+1
special_node_count_one = True
comp = defaultdict(int)