z1=z1,
mz2=mz2,
z2=z2)
if modified:
print t.get('id')
if (pid, z1, spectra) not in tgroup:
tgroup[(pid, z1, spectra)] = dict(transitions=[],
nrt=nrt,
rt=rt,
mz1=mz1,
scans=scans)
tgroup[(pid, z1, spectra)]['transitions'].append((t.get('id'), relint))
for pid, z1, spectra in tgroup:
tgroup[(pid, z1, spectra)]['ntransition'] = len(
tgroup[(pid, z1, spectra)]['transitions'])
tg, mod = w.addtransgroup(peptide=pid,
z1=z1,
spectra=spectra,
**tgroup[(pid, z1, spectra)])
if mod:
print tg.get('id')
if tg.get('id') in spectra2tg[spectra]:
spectra2tg[spectra].remove(tg.get('id'))
for spectra in allspectra:
for tgid in spectra2tg[spectra]:
print "Deleting transition group", tgid
w.delete(tgid)
#!/bin/env python27
from getwiki import GPTWiki, Peptide
import sys
from collections import defaultdict
w = GPTWiki()
for sp in sys.argv[1:]:
for tg in w.iterspectgs(sp):
if not tg:
continue
print >> sys.stderr, "Delete transition group", tg.get('id')
w.delete(tg.get('id'))
print >> sys.stderr, "Delete spectra", sp
w.delete(sp)
#!/bin/env python27
from getwiki import GPTWiki, Peptide
import sys
from collections import defaultdict
w = GPTWiki()
for tgpage in w.iterpages(include_categories=['TransitionGroup']):
tg = w.get(tgpage.name)
if tg.get('spectra') in sys.argv[1:]:
print >> sys.stderr, "Delete transition group", tgpage.name
w.delete(tgpage.name)
for sp in sys.argv[1:]:
print >> sys.stderr, "Delete spectra", sp
w.delete(sp)
#!/bin/env python27
from getwiki import GPTWiki, Peptide
import sys
from collections import defaultdict
w = GPTWiki()
currtrans = set()
for tgpage in w.iterpages(include_categories=['TransitionGroup']):
tg = w.get(tgpage.name)
tgid = tg.get('id')
for t, i in tg.get('transitions'):
tr = w.get(t)
if tr:
currtrans.add(t)
for tpage in w.iterpages(include_categories=['Transition']):
t = w.get(tpage.name)
tid = t.get('id')
if tid not in currtrans:
print >> sys.stderr, "Delete transition " + tid
w.delete(tid)
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())
#!/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)
