z1=z1, spectra=spectra, mz1=mz1, nrt=nrt, rt=rt, prt=rt, transitions=trans, ntransition=len(trans), **extras) if 'lccalibration' in data and spectra not in lccal: nrtslope, nrtintercept = map(float, data['lccalibration'].split(":")) lccal[spectra]['nrtslope'] = nrtslope lccal[spectra]['nrtintercept'] = nrtintercept tgs[spectra].add(tg.get('id')) for spectra in allspec: spec = w.get(spectra) if spectra in lccal: spec.set("nrtslope", lccal[spectra]['nrtslope']) spec.set("nrtintercept", lccal[spectra]['nrtintercept']) else: spec.delete("nrtslope") spec.delete("nrtintercept") w.put(spec) for tg in w.itertgs(spectra=spectra, all=True): if tg.get('id') not in tgs[spectra]: if w.cleartransgroup(tg): print "Clear", tg.get("id")
w = GPTWiki() # if len(sys.argv) < 2: # print 'please enter the spectra file name regex' # exit(1) for spectrapage in w.iterspec(acqtype="DDA"): # if not re.search(sys.argv[1],spectrapage.get('name')): # continue print spectrapage.get('name') nrtslope = spectrapage.get('nrtslope') nrtintercept = spectrapage.get('nrtintercept') if not nrtslope or not nrtintercept: print "No NRT slope or intercept" continue for tgpage in w.itertgs(spectra=spectrapage.get('name')): tgid = tgpage.get('id') peakrt = tgpage.get('prt') nrt = 0.0 if peakrt != None: nrt = (peakrt - nrtintercept) / nrtslope tgpage.set('nrt', nrt) if w.put(tgpage): print tgid else: tgpage.set('nrt', '') if w.put(tgpage): print tgid
seen = set() for praccfile in sys.argv[1:]: for pracc in open(praccfile): pracc = pracc.strip() if pracc in seen: continue # print >>sys.stderr, pracc seen.add(pracc) data = urllib.urlopen('http://www.uniprot.org/uniprot/' + pracc + '.xml') for seq_record in Bio.SeqIO.parse(data, 'uniprot-xml'): desc = seq_record.description pracc1 = seq_record.id seq = str(seq_record.seq) gene = seq_record.annotations['gene_name_primary'] sys.stdout.write(seq_record.format('fasta')) break name = gene seqlines = [] for i in range(0, len(seq), 60): seqlines.append(seq[i:i + 60]) seq = "\n".join(seqlines) p = Protein(accession=pracc1, description=desc, gene=gene, sequence=seq, species='H**o sapiens', name=name) if w.put(p): print >> sys.stderr, pracc1
#!/bin/env python2 from getwiki import GPTWiki import time, sys w = GPTWiki() for sp in w.iterspec(method=sys.argv[1]): sp.set('inst', sys.argv[2]) sp.set('type', sys.argv[3]) if w.put(sp): print sp.get('id')
#!/bin/env python27 from getwiki import GPTWiki import re w = GPTWiki() monos = "NHSF" for gly in w.iterglycans(): gsym = gly.get('sym') mcnt = {} for mono in monos: mcnt[mono] = 0 m = re.search(mono + r'(\d+)', gsym) if m: mcnt[mono] = int(m.group(1)) elif mono in gsym: mcnt[mono] = 1 gly.set('nneuac', mcnt['S']) if w.put(gly): print gly.get('id') for pep in w.iterpeptides(): pepname = pep.get('name') pep.set('nox', pepname.count('[Ox]')) if w.put(pep): print pep.get('id')
plt.legend() plt.title(s) plt.xlabel('Peptide NRT') plt.ylabel('Peak RT(min)') plt.savefig(s + '.coefficients.png') plt.show() plt.close() f.write('\t'.join( map(str, ['filename', 'nrtobsgt0', 'slope', 'intercept', 'r_value'])) + '\n') f.write(s + '\t' + str(nrtobsgt0[s]) + '\t' + str(round(slope, 4)) + '\t' + str(round(intercept, 2)) + '\t' + str(round(r_value, 4)) + '\n') if raw_input('Write to wiki? ').lower()[0] == "y": spectrapage = w.get(s) # # if nrtobsgt0[s] == 1 or slope < 0.37 or slope > 0.41: # spectrapage.set('nrtslope','') # spectrapage.set('nrtintercept','') # if w.put(spectrapage): ## # print 'spectrapage is updated:',s # pass # continue spectrapage.set('nrtslope', float(slope)) spectrapage.set('nrtintercept', float(intercept)) if w.put(spectrapage): # print 'spectra is updated:',s pass # f.close()
#!/bin/env python2 from getwiki import GPTWiki, Peptide, ProteinSite import sys w = GPTWiki() for pep in w.iterpep(): for al in pep.get('alignments', []): pr = al.get('protein') prsites = al.get('prsites', "").split('|') for prs in prsites: aa = prs[0] pos = int(prs[1:]) ps = ProteinSite(protein=pr, aa=aa, position=pos) if w.put(ps): print ProteinSite.pagename(protein=pr, aa=aa, position=pos) al.append('site', ps) # al.delete('prsites') if w.put(pep): print pep.get('id')
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())
for pepid in sorted((set(origpepnrt) - set(newpepnrt))): print pepid, round(origpepnrt[pepid], 3), round(oldresid[pepid], 3), "lost" for pepid in sorted((set(newpepnrt) - set(origpepnrt))): print pepid, round(newpepnrt[pepid], 3), round(newresid[pepid], 3), "gained" if not opts.upload: sys.exit(0) w = GPTWiki(quiet=True) for tg in w.itertransgroups(): tgid = tg.get('id') if tgid in badtg: tg.set('pepnrt', 'drop') elif tgid in alltg: tg.set('pepnrt', 'use') else: tg.delete('pepnrt') if w.put(tg): print tgid for pep in w.iterpeptides(): pepid = pep.get('id') if pepid in newpepnrt: if isinstance(newpepnrt[pepid], float): pep.set('nrt', newpepnrt[pepid]) else: pep.delete('nrt') if w.put(pep): print pepid
if raw_input("Upload? ") not in ("Y", "y"): sys.exit(0) w = GPTWiki(quiet=True) for spec in w.iterspec(acqtype="DDA"): print spec.get("name") for tg in w.itertgs(spectra=spec.get("name")): tgid = tg.get('id') if tgid in badtg: tg.set('pepnrt', 'drop (%+.3f)' % (badresid[tgid])) elif tgid in alltg: tg.set('pepnrt', 'use (%+.3f)' % (goodresid[tgid])) else: tg.delete('pepnrt') if opts.upload and w.put(tg): print tgid for pep in w.iterpeptides(): pepid = pep.get('id') if newpepnrt.get(pepid) != None: pep.set('nrt', newpepnrt[pepid]) pep.set('nrtobs', newpepnrtobs[pepid]) elif False and pepid in goodpepids and pepfits.get(pepid) != None: pep.set('nrt', pepfits[pepid]) pep.set('nrtobs', 0) else: pep.delete('nrt') pep.delete('nrtobs') if opts.upload and w.put(pep): print pepid