if it <= 0:
continue
trans.append((trid, it))
trans.sort(key=lambda t: -t[1])
pepid = data['trlib_pepid']
z1 = data['trlib_z1']
mz1 = data['trlib_mz1']
extras = {}
for key in ("intensity", "score", "extraction", "fdr"):
if key in data:
extras[key] = data[key]
tg, mod = w.addtransgroup(peptide=pepid,
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'])
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)
