import sys, urllib, string from collections import defaultdict nrtonly = False if len(sys.argv) > 1 and sys.argv[1] == "nrtonly": nrtonly = True w = GPTWiki() seenpeps = set() sites = set() prot2site = defaultdict(set) samples = set() glycans = set() glysites = set() site2gly = defaultdict(set) for sp in w.iterspec(type='DDA'): for tg in w.itertgs(spectra=sp.get('name')): tgid = tg.get('id') if tg.get('peptide') in seenpeps: continue pep = w.get(tg.get('peptide')) if nrtonly and pep.get('nrt') == None: continue seenpeps.add(pep.get('id')) gly = pep.get('glycan')[0][0] glycans.add(gly) for al in pep.get('alignments', []): site = al.get('prsites') prot = al.get('protein') print pep.get('id'), prot, site, gly sites.add((prot, site))
#!/bin/env python2 from getwiki import GPTWiki import sys, re 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', '')
#!/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')
nmono += 1 else: nmono += int(kvpairs[i + 1]) return nmono def label2series(lab): return lab[0].lower() w = GPTWiki() peps = defaultdict(lambda: defaultdict(dict)) for sp in w.iterspec(sample=opts.sample, acqtype=opts.acqtype, method=opts.method, inst=opts.inst): print >> sys.stderr, sp.get('name') for i, tg in enumerate(w.itertgs(spectra=sp.get('name'))): pep = w.get(tg.get('peptide')) pepid = pep.get('id') if pep.get('nrt') == None: continue z1 = tg.get('z1') ntrans = len(tg.get('transitions', [])) if ntrans == 0: continue proteins = set() for al in pep.get("alignments", []): proteins.add(al.get("protein")) for trid, trint in tg.get('transitions', []):
if opts.cachefile and os.path.exists(opts.cachefile): data = json.loads(open(opts.cachefile).read()) tgrows = data['tgrows'] peprows = data['peprows'] tgs = data['tgs'] origpepnrt = data['pepnrt'] else: monos = "NHFS" tgs = dict() origpepnrt = dict() tgrows = [] peprows = [] pepseen = set() w = GPTWiki(quiet=True) for spec in w.iterspec(acqtype="DDA"): print spec.get("name") for tg in w.itertgs(spectra=spec.get("name")): pepid = tg.get('peptide') p = w.get(pepid) pepacc = p.get('id') pepseq = p.get('sequence') pepname = p.get('name') pepnrt = p.get('nrt') pepnrtobs = int(p.get('nrtobs', 0)) if pepnrtobs == 0: pepnrt = None nrt = tg.get('nrt') if nrt is None and pepnrt is None: continue glyacc = p.get('glycan')[0][0]