class GlyIUPACFilter:
def __init__(self, glydb):
self.glydb = glydb
self.fmt = IUPACLinearFormat()
def __iter__(self):
return self.next()
def next(self):
for gr in self.glydb:
try:
iupac = self.fmt.toStr(gr.glycan)
gr['IUPAC'] = iupac
except KeyError:
pass
yield gr
class LinearIUPACDatabase:
extn = 'iupac'
source = ""
prefix = ""
def __init__(self, filename):
self.filename = filename
self.name, extn = filename.rsplit('.', 1)
assert extn == self.extn
self.fmt = IUPACLinearFormat()
def __iter__(self):
return self.next()
def preprocess(self, glystr):
return glystr
def next(self):
h = open(self.filename)
seenaccs = set()
for lineno, l in enumerate(h):
if lineno == 0:
continue
if l.startswith('#'):
continue
sl = map(str.strip, l.split(None, 1))
acc = self.acc(sl[0])
glystr = self.preprocess(sl[1])
if acc in seenaccs:
continue
seenaccs.add(acc)
try:
g = self.fmt.toGlycan(glystr)
except IUPACLinearParseError:
traceback.print_exc()
continue
yield GlyRecord(source=self.source,
accession=self.prefix + acc,
glycan=g,
name=self.name)
h.close()
class CFGArrayDatabase:
def __init__(self, filename):
self.filename = filename
self.name, extn = filename.rsplit('.', 1)
assert extn == 'cfg'
self.fmt = IUPACLinearFormat()
def __iter__(self):
return self.next()
def next(self):
h = open(self.filename)
for lineno, l in enumerate(h):
if lineno == 0:
continue
if l.startswith('#'):
continue
sl = l.split(None, 1)
acc = int(sl[0])
glystr = sl[1].strip()
# Wow - badly hand formatted CFG IUPAC linear glycans suck...
m = re.search(r'([ab]1?)?-?(\d(-?))?([RS][pP]?\d+|MDPLys)?$',
glystr)
if m != None:
x = len(m.group(0))
glystr = glystr[:-x]
try:
g = self.fmt.toGlycan(glystr)
except IUPACLinearParseError:
traceback.print_exc()
continue
print >> sys.stderr, ">>CFG%03d" % acc
yield GlyRecord(source="CFGArray",
accession="CFG%03d" % acc,
glycan=g,
name=self.name)
def __init__(self, filename):
self.filename = filename
self.name, extn = filename.rsplit('.', 1)
assert extn == 'cfg'
self.fmt = IUPACLinearFormat()
m = re.search(r'([ab]1?)?-?(\d(-?))?([RS][pP]?\d+|MDPLys)?$',
glystr)
if m != None:
x = len(m.group(0))
glystr = glystr[:-x]
try:
g = self.fmt.toGlycan(glystr)
except IUPACLinearParseError:
traceback.print_exc()
continue
print >> sys.stderr, ">>CFG%03d" % acc
yield GlyRecord(source="CFGArray",
accession="CFG%03d" % acc,
glycan=g,
name=self.name)
if __name__ == '__main__':
import sys
from GlycanFormatter import IUPACLinearFormat
fmt = IUPACLinearFormat()
fmt1 = GlycoCTFormat()
gdb = CFGArrayDatabase(sys.argv[1])
for r in gdb:
lc = fmt.toStr(r.glycan)
print r.accession, lc
# print fmt1.toStr(r.glycan)
# print r.glycan
print r.glycan
sys.stdout.flush()
def __init__(self, glydb):
self.glydb = glydb
self.fmt = IUPACLinearFormat()