#!/bin/env python27
import sys
from getwiki import GPTWiki
w = GPTWiki()
if len(sys.argv) > 1:
if sys.argv[1] == "-":
for p in w.iterpages(exclude_categories=[
'Transition', 'Peptide', 'Protein', 'TransitionGroup', 'Glycan'
]):
print >> sys.stderr, p.name
w.refresh(p)
elif sys.argv[1] in ('Transition', 'Peptide', 'Protein', 'Glycan',
'TransitionGroup'):
for p in w.iterpages(include_categories=sys.argv[1:]):
print >> sys.stderr, p.name
w.refresh(p)
else:
for p in w.iterpages(regex=sys.argv[1]):
print >> sys.stderr, p.name
w.refresh(p)
else:
fromwiki = sys.argv[1].upper()
towiki = sys.argv[2].upper()
assert fromwiki in ("PROD", "DEV", "TEST")
assert towiki in ("PROD", "DEV", "TEST")
assert fromwiki != towiki
w1 = GPTWiki(smwenv=fromwiki, quiet=True)
print >> sys.stderr, "from: %s" % (w1.title(), )
w2 = GPTWiki(smwenv=towiki, quiet=True)
print >> sys.stderr, " to: %s" % (w2.title(), )
dummy = raw_input("Enter to proceed, <Ctrl-C> to abort:")
currentids = set()
for page in w1.iterpages(include_categories=('Transition', 'Peptide',
'TransitionGroup')):
id = page.name
currentids.add(id)
it = w1.get(id)
if w2.put(it):
print >> sys.stderr, "Pushing %s to %s" % (id, w2.title())
else:
print >> sys.stderr, "No change to %s in %s" % (id, w2.title())
for page in w2.iterpages(include_categories=('Transition', 'Peptide',
'TransitionGroup')):
id = page.name
if id not in currentids:
w2.delete(id)
print >> sys.stderr, "Delete %s from %s" % (id, w2.title())
import sys, urllib, string, csv, os.path
from collections import defaultdict
import Bio.SeqIO
from util import peptide_mw, mod_mw
def asscan(s):
t = s.rstrip(')').split('(')
return [int(t[0])] + t[1].split(',')
w = GPTWiki()
spectra2tg = defaultdict(set)
for tgpage in w.iterpages(include_categories=['TransitionGroup']):
tg = w.get(tgpage.name)
spectra = tg.get('spectra')
spectra2tg[spectra].add(tg.get('id'))
allspectra = set()
for transfile in sys.argv[1:]:
spectra, sample, method, index, extn = transfile.rsplit('.', 4)
spectra = os.path.split(spectra)[1]
allspectra.add(spectra)
w.addacquisition(name=spectra, method=method, sample=sample)
tgroup = defaultdict(dict)
for l in csv.DictReader(open(transfile), dialect='excel-tab'):
seq = l['PeptideSequence']
glyspec = l['Glycans']
#!/bin/env python27
from getwiki import GPTWiki, Peptide
import sys, urllib, string
import Bio.SeqIO
from util import peptide_mw, mod_mw
seen = set()
w = GPTWiki()
peps = []
for p in w.iterpages(include_categories=['Peptide']):
pep = w.get(p.name)
pepkey = Peptide.key(pep.get('sequence'), pep.get('glycan', []),
pep.get('mod', []))
if pepkey in seen:
print >> sys.stderr, p.name
w.delete(p.name)
seen.add(pepkey)