from pygly.GlycanImage import GlycanImage
from pygly.GlyTouCan import GlyTouCan
if len(sys.argv) <= 1:
print >> sys.stderr, "glyimg.py [ image options ] <gtc-accession> [ <gtc-accession> ... ]"
print >> sys.stderr, """
Image options:
scale <float> [1.0]
reducing_end (true|false) [true]
orientation (RL|LR|TB|BT) [RL]
notation (cfg|cfgbw|cfglink|uoxf|text|uoxfcol) [cfg]
display (normal|normalinfo|compact) [normalinfo]
""".strip()
sys.exit(1)
gtc = GlyTouCan(usecache=True)
imageWriter = GlycanImage()
lastopt = 0
for i in range(1, len(sys.argv), 2):
if sys.argv[i].startswith('G'):
break
key = sys.argv[i]
value = sys.argv[i + 1]
imageWriter.set(key, value)
lastopt = i + 1
for acc in sys.argv[(lastopt + 1):]:
outfile = acc + ".png"
g = gtc.getGlycan(acc)
imageWriter.writeImage(g, outfile)
#!/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, traceback
from getwiki import GlycoMotifWiki, CCRCMotif
w = GlycoMotifWiki()
from pygly.GlyTouCan import GlyTouCan
gtc = GlyTouCan()
from gtccache import GlyTouCanCache
gtccache = GlyTouCanCache()
from dataset import XLSXFileTable
rows = XLSXFileTable(sys.argv[1])
current = set()
for r in rows:
try:
index = int(r['#'])
except ValueError:
traceback.print_exc()
continue
name = r['Trivial Name-Cummings']
if name:
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
import os, sys
import json
import findpygly
from pygly.GlycanFormatter import GlycoCTFormat, WURCS20Format
from pygly.GlyTouCan import GlyTouCan
g = GlyTouCan()
wurcs_parser = WURCS20Format()
glycoct_parser = GlycoCTFormat()
wpath = "dumps/wurcs"
gpath = "dumps/glycoct"
wlist = os.listdir(wpath)
glist = os.listdir(gpath)
alllist = list(set(wlist+glist))
print "Total glycan number %s" % len(alllist)
glycanobj = {}
for filename in alllist:
acc = filename.rstrip(".txt")
try:
gseq = open(os.path.join(gpath, filename)).read().strip()
obj = glycoct_parser.toGlycan(gseq)
except:
try:
#!/bin/env python27
import sys, traceback
from getwiki import GlycoMotifWiki, UniCarbMotif
w = GlycoMotifWiki()
from pygly.GlyTouCan import GlyTouCan
gtc = GlyTouCan()
from gtccache import GlyTouCanCache
gtccache = GlyTouCanCache()
from pygly.GlycanFormatter import GlycoCTFormat, IUPACParserExtended1
gparser = GlycoCTFormat()
imparser = IUPACParserExtended1()
from dataset import XLSXFileTable
rows = XLSXFileTable(sys.argv[1])
possibleaglycon = ["Cer", "R", "Ser/Thr"]
reaglycon = ["Ser/Thr", "Cer", "Other"]
current = set()
for r in rows:
id = r["ID"]
name = r["Name"]
iupacseq = r["IUPAC"]
accession = "%06d" % id
if not iupacseq:
continue
#!/usr/bin/env python27
import sys, os, os.path
import findpygly
from pygly.GlyTouCan import GlyTouCan
from pygly.GlycanFormatter import GlycoCTFormat
glycoct_format = GlycoCTFormat()
gtc = GlyTouCan()
for l in sys.stdin:
acc = l.strip()
g = gtc.getGlycan(acc)
if g and g.fully_determined():
print acc, True
if not os.path.exists('%s.txt' % (acc, )):
seq = gtc.getseq(acc, 'glycoct')
if not seq:
try:
seq = glycoct_format.toStr(g)
except:
pass
if seq:
wh = open('%s.txt' % (acc, ), 'w')
wh.write(seq.strip() + '\n')
wh.close()
else:
print acc, (False if g else None)
#!/bin/env python27
import sys, traceback, os, csv
from getwiki import GlycoMotifWiki
from getwiki import GlydinMotif, GlydinCummingsMotif, GlydinHayesMotif, GlydinCermavMotif, GlydinSugarbindMotif, GlydinBioligoMotif
w = GlycoMotifWiki()
from dataset import XLSXFileTable
rows = XLSXFileTable(sys.argv[1])
from pygly.GlyTouCan import GlyTouCan
gtc = GlyTouCan()
from gtccache import GlyTouCanCache
gtccache = GlyTouCanCache()
"""
[x]collection structure
key: id (not row number)
value: {"aglycon":"String"/None, "name":""/None, "gtcid":""}
"""
ccollection = {}
hcollection = {}
vcollection = {}
sbcollection = {}
bcollection = {}
collections = {
"c": ccollection,
"h": hcollection,