class GlyTouCanUtil(object):
_wurcs_mono_format = WURCS20MonoFormat()
_wurcs_format = WURCS20Format()
_glycoct_format = GlycoCTFormat()
_alphamap = None
def getUnsupportedCodes(self, acc):
codes = set()
substs = set()
invalid = set()
other = set()
sequence = self.getseq(acc, 'wurcs')
if not sequence:
return codes, substs, invalid, other
monos = sequence.split('/[', 1)[1].split(']/')[0].split('][')
for m in monos:
try:
g = self._wurcs_mono_format.parsing(m)
except UnsupportedSkeletonCodeError as e:
codes.add(e.message.rsplit(None, 1)[-1])
except UnsupportedSubstituentError as e:
substs.add(e.message.rsplit(None, 1)[-1])
except InvalidMonoError as e:
invalid.add(e.message.rsplit(None, 1)[-1])
except GlycanParseError:
pass
try:
g = self._wurcs_format.toGlycan(sequence)
except ZeroPlusLinkCountError:
other.add("0+ link count")
except UndeterminedLinkCountError:
other.add("undetermined link count")
except CircularError:
other.add("circular")
except LinkCountError:
other.add("bad link count")
except GlycanParseError:
pass
return codes, substs, invalid, other
def getGlycan(self, acc, format=None):
if not format or (format == 'wurcs'):
sequence = self.getseq(acc, 'wurcs')
if sequence:
try:
return self._wurcs_format.toGlycan(sequence)
except GlycanParseError:
pass # traceback.print_exc()
if not format or (format == 'glycoct'):
sequence = self.getseq(acc, 'glycoct')
if sequence:
try:
return self._glycoct_format.toGlycan(sequence)
except GlycanParseError:
pass
return None
def glycoct(self, acc, fetch=None):
g = self.getGlycan(acc, fetch)
if not g:
return None
try:
return g.glycoct()
except RuntimeError:
pass
return None
def umw(self, acc, fetch=None):
g = self.getGlycan(acc, fetch)
if not g:
return None
try:
return g.underivitized_molecular_weight()
except (LookupError, ValueError):
pass
return None
def wurcs2glycoct(self, acc):
sequence = self.getseq(acc, 'wurcs')
if sequence:
sequence1 = urllib.parse.quote_plus(sequence)
url = 'https://api.glycosmos.org/glycanformatconverter/2.3.2-snapshot/wurcs2glycoct/' + sequence1
try:
data = json.loads(urllib.request.urlopen(url).read())
if 'GlycoCT' in data:
return data['GlycoCT']
except ValueError:
pass
return None
def subsumptionbyapi(self, acc):
sequence = self.getseq(acc, 'wurcs')
if sequence:
sequence1 = urllib.parse.quote_plus(sequence)
url = 'https://api.glycosmos.org/subsumption/0.2.0/' + sequence1
data = urllib.request.urlopen(url).read()
seen = set()
lasts = None
for triple in sorted([
tuple([
s.strip() for s in list(
map(str, list(map(t.get, ("S", "P", "O")))))
]) for t in json.loads(data)
]):
if triple in seen:
continue
seen.add(triple)
if triple[0] != lasts:
if lasts != None:
print("")
print(triple[0])
lasts = triple[0]
if triple[2] == sequence:
print(">> " + "\t".join(triple[1:]))
else:
print(" " + "\t".join(triple[1:]))
def findskel(self, skel, maxcount=None):
if maxcount != None:
maxcount = int(maxcount)
for acc, format, wurcs in self.allseq(format='wurcs'):
glycoct = self.getseq(acc, format='glycoct')
if not glycoct:
continue
monos = wurcs.split('/[', 1)[1].split(']/')[0].split('][')
if maxcount != None and len(monos) > maxcount:
continue
for mono in monos:
msk = re.search(r'^(.*?)([-_].*)?$', mono).group(1)
assert msk
m = re.search(r"^%s$" % (skel, ), msk)
if m:
yield acc, m.group(0)
def multiseq(self):
counts = defaultdict(set)
for acc, fmt, seq in self.allseq():
counts[(acc, fmt)].add(seq)
for k, v in list(counts.items()):
if len(v) > 1:
yield k
def fixcompwurcs(self, wurcsseq, subst=[]):
if not self._alphamap:
self._alphamap = dict()
for i, c in enumerate(range(ord('a'), ord('z') + 1)):
self._alphamap[i + 1] = chr(c)
self._alphamap[chr(c)] = (i + 1)
for i, c in enumerate(range(ord('A'), ord('Z') + 1)):
self._alphamap[i + 1 + 26] = chr(c)
self._alphamap[chr(c)] = (i + 1 + 26)
prefix, counts, rest = wurcsseq.split('/', 2)
unodes, nodes, edges = counts.split(',')
nodes = int(nodes)
assert '0+' in edges
edges = (nodes - 1)
ambignode = "|".join(
["%s?" % (self._alphamap[i], ) for i in range(1, nodes + 1)])
ambigedge = "%s}-{%s" % (ambignode, ambignode)
ambigedges = [ambigedge] * edges
if hasattr(subst, 'items'):
subst = list(subst.items())
for sub, cnt in subst:
for i in range(cnt):
ambigedges.insert(0, "%s}%s" % (ambignode, sub))
return "%s/%s,%d,%d/%s%s" % (prefix, unodes, nodes, len(ambigedges),
rest, "_".join(ambigedges))
def anyglycan2wurcs(self, glycan):
sequence = ""
if isinstance(glycan, Glycan.Glycan):
if not self.glycoct_format:
self.glycoct_format = GlycoCTFormat()
sequence = self.glycoct2wurcs(self.glycoct_format.toStr(glycan))
if '0+' in sequence:
sequence = self.fixcompwurcs(sequence)
else:
sequence = re.sub(r'\n\n+', r'\n', glycan)
if sequence.strip().startswith('RES'):
sequence = self.glycoct2wurcs(glycan)
return sequence
def glycoct2wurcs(self, seq):
requestURL = "https://api.glycosmos.org/glycanformatconverter/2.3.2-snapshot/glycoct2wurcs/"
encodedseq = urllib.parse.quote(seq, safe='')
requestURL += encodedseq
req = urllib.request.Request(requestURL)
# self.wait()
response = urllib.request.urlopen(req).read()
result = json.loads(response)
try:
wurcs = result["WURCS"]
except:
raise ValueError("GlycoCT 2 WURCS conversion failed")
return wurcs.strip()
#!/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)
for r in rows:
id = r["ID"]
name = r["Name"]
iupacseq = r["IUPAC"]
accession = "%06d" % id
if not iupacseq:
continue
if "n-" in iupacseq:
print "%s Contains repeats" % accession
continue
try:
gobj = imparser.toGlycan(iupacseq)
glycoct = gparser.toStr(gobj)
wurcs = gtc.glycoct2wurcs(glycoct)
glytoucan = gtc.register(wurcs)[0]
except:
print "%s is not able to load to Glycomotif" % accession
print iupacseq
continue
aglycon = None
redend = None
for agly in possibleaglycon:
if agly in iupacseq:
aglycon = agly
if aglycon in reaglycon:
redend = True
key = sys.argv[i]
try:
value = sys.argv[i + 1]
value = float(sys.argv[i + 1])
value = int(sys.argv[i + 1])
except ValueError:
pass
getargs[key] = value
if count:
cnt = gdb.count(**getargs)
print dbname, cnt
elif glycoct:
fmt1 = GlycoCTFormat()
zf = ZipFile(dbname.rsplit('.', 1)[0] + '.gct', 'w', ZIP_DEFLATED)
for r in gdb.get(**getargs):
zf.writestr("%s.txt" % r.accession, fmt1.toStr(r.glycan))
zf.close()
else:
fmt = LinearCodeFormat()
for r in gdb.get(**getargs):
if r['lincode']:
lc = fmt.toStr(r.glycan)
print r.accession, r['nlinked'], r.get(
'oxford', "-"), r['molecular_weight'], r['composition'], lc
print r
else:
print r.accession, r['nlinked'], r.get(
'oxford', "-"), r['molecular_weight'], r['composition']
print r
else:
print >> sys.stderr, "Bad command:" + sys.argv[1]