print 'please enter the spectra file name(s)' exit(1) spectrafiles = sys.argv[1:] w = GPTWiki() # outfile = open('../data/'+sys.argv[1][:5]+'.fitall.txt','w') outfile = sys.stdout outfile.write('\t'.join( map(str, [ 'TransGroup', 'Spectra', 'PeptideID', 'PrecZ', 'mmu', 'ExpRT', 'AdjRT', 'R_Value', 'Std_Dev', 'Height', 'FWHM', 'Area', '\n' ]))) for tg in w.itertransgroups(): tgid = tg.get('id') pepid = tg.get('peptide') z1 = tg.get('z1') exprt = tg.get('rt') spectra = tg.get('spectra') if spectra not in spectrafiles: continue scans = tg.get('scans') hcds = [] HCDs = {} for i, s in enumerate(scans): try: j = s.index('HCD') hcds.append(float(s[j + 1]))
#!/bin/env python2 import sys from collections import defaultdict from getwiki import GPTWiki w=GPTWiki() tla = {'N': 'Asn'} sampleids = set(sys.argv[1:]) prsites = defaultdict(dict) for i,tg in enumerate(w.itertransgroups()): pep = w.get(tg.get('peptide')) # if not pep.get('nrt'): # continue glyid = pep.get('glycan')[0][0] gly = w.get(glyid) name = "" for n in gly.get('name',[]): if 'Fuc' in n: continue if 'HexNAc' in n: name = n break cls = gly.get('class') if len(cls) != 1: continue cls = cls[0]
import numpy as np from scipy import stats import sys w = GPTWiki() if len(sys.argv) < 2: print 'please enter the spectra file name(s)' exit(1) spectrafiles = sys.argv[1:] pepnrtpairs = defaultdict(list) nrtobsgt0 = {} for tgpage in w.itertransgroups(): spectra = tgpage.get('spectra') if spectra not in spectrafiles: continue tgid = tgpage.get('id') pepid = tgpage.get('peptide') peppage = w.get(pepid) pepnrt = peppage.get('nrt') nrtobs = peppage.get('nrtobs') peakrt = tgpage.get('prt') if peakrt != None and pepnrt != None: if nrtobs == '0': continue else: