import numpy as np
import getwiki
from analysis.fisher import lod, fisher_exact_low, fisher_exact_high
from transitionspecificity import specscore
w = GPTWiki()
trspec = {}
labelspec = {}
glycanlabelspec = {}
smallwindow = 1
largewindow = 6
threshold = 50
nonspeccount = 0
alltrs = set()
for tg in w.itertgs(acqtype='DIA'):
pepid = tg.get('peptide')
pepage = w.get(pepid)
z1 = tg.get('z1')
spectra = tg.get('spectra')
if spectra.find('DIA') == -1:
continue
try:
glycan = re.search('\[H(.)*?\]', pepage.get('name')).group(0)[1:-1]
except:
continue
filename = pepid + '.' + str(z1) + '.50.json'
onlinefile = 'http://edwardslab.bmcb.georgetown.edu/~nedwards/dropbox/pBYmLSkGeq/' + spectra + '/' + filename
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))
prot2site[prot].add(site)
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
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', []):
tr = w.get(trid)
if trid not in peps[(pepid, z1)]:
peps[(pepid, z1)][trid]['pepname'] = pep.get('name')
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]
g = w.get(glyacc)
gsym = g.get('sym')
