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)