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:
