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
