#!/bin/env python2
import sys
from collections import defaultdict
from getwiki import GlycanData, Glycan
w = GlycanData()
# print >>sys.stderr, "Read subsumption graph"
from pygly.GNOme import SubsumptionGraph
gnome = SubsumptionGraph()
gnome.loaddata(sys.argv[1])
gnomeacc = set()
for n in gnome.nodes():
gnomeacc.add(n)
accs = set()
for fn in sys.argv[2:]:
accs.update(open(fn).read().split())
for m in w.iterglycan():
acc = m.get('accession')
m.delete_annotations(type="Subsumption")
if acc in gnomeacc:
m.set_annotation(value=acc,
property="GNOme",
source="GNOme",
#!/bin/env python27
import sys
import findpygly
from pygly.GNOme import GNOme, SubsumptionGraph
from pygly.GlyTouCan import GlyTouCan
g = SubsumptionGraph()
g.readfile(sys.argv[1])
sys.argv.pop(1)
# g = GNOme()
gtc = GlyTouCan(usecache=True)
for acc in sys.argv[1:]:
taccs = set(filter(g.istopology, g.descendants(acc)))
# print " ".join(sorted(taccs))
toremove = set()
for tacc in taccs:
gly = gtc.getGlycan(tacc)
if gly.undetermined():
toremove.add(tacc)
for m in gly.all_nodes():
if m.stem() == None:
toremove.add(tacc)
break
for tacc in toremove:
taccs.remove(tacc)
toremove = set()
for tacc in taccs:
#!/bin/env python27
import sys
from collections import defaultdict
import findpygly
# use the current raw GNOme subsumption dump
# Back-fill with GlyTouCan if needed.
from pygly.GNOme import SubsumptionGraph
gnome = SubsumptionGraph()
gnome.loaddata(sys.argv[1])
sys.argv.pop(1)
accs = set()
for f in sys.argv[1:]:
accs.update(open(f).read().split())
newaccs0 = set(accs)
while True:
newaccs = set()
for acc in newaccs0:
newaccs.add(acc)
newaccs.update(
filter(lambda anc: anc.startswith('G'), gnome.ancestors(acc)))
topo = gnome.get_topology(acc)
comp = gnome.get_composition(acc)
#!/bin/env python2
import sys
from operator import itemgetter
from collections import defaultdict
from getwiki import GlycanData, Glycan
w = GlycanData()
from pygly.GNOme import SubsumptionGraph
gnome = SubsumptionGraph()
gnome.loaddata(sys.argv[1])
sys.argv.pop(1)
def iterglycan():
if len(sys.argv) > 1:
seen = set()
for acc in sys.argv[1:]:
if acc in seen:
continue
m = w.get(acc)
if m:
seen.add(acc)
yield m
for desc in gnome.descendants(acc):
if desc in seen:
continue
m = w.get(desc)
if m:
#!/bin/env python2
import sys
from operator import itemgetter
from collections import defaultdict
from getwiki import GlycanData, Glycan
w = GlycanData()
from pygly.GNOme import SubsumptionGraph
gnome = SubsumptionGraph()
gnome.loaddata(sys.argv[1])
sys.argv.pop(1)
debug = False
def iterglycan():
global debug
if len(sys.argv) > 1:
for acc in sys.argv[1:]:
m = w.get(acc)
if m:
debug = True
yield m
else:
for m in w.iterglycan():
yield m
from clseng import ClassifierEngine
classifier = ClassifierEngine()
acc2type = defaultdict(set)
#!/bin/env python27
import sys
from collections import defaultdict
from getwiki import GlycanData, Glycan
w = GlycanData()
# print >>sys.stderr, "Read subsumption graph"
from pygly.GNOme import SubsumptionGraph
gnome = SubsumptionGraph()
gnome.loaddata(sys.argv[1])
accs = set()
for fn in sys.argv[2:]:
accs.update(open(fn).read().split())
for m in w.iterglycan():
acc = m.get('accession')
m.delete_annotations(type="Subsumption")
if gnome.isbasecomposition(acc):
m.set_annotation(property="Level",
value="BaseComposition",
source="GNOme",
type="Subsumption")
m.set_annotation(property="BaseComposition",
value=acc,
source="GNOme",