method, anfrac = method.split(':')
else:
anfrac = None
tgs = defaultdict(set)
allspec = set()
lccal = defaultdict(dict)
for specfile in sys.argv[3:]:
dirname = specfile.rsplit('.', 2)[0]
if dirname.endswith('.centroid'):
dirname = dirname.rsplit('.', 1)[0]
spectra = os.path.split(dirname)[1]
allspec.add(spectra)
w.addacquisition(name=spectra,
method=method,
anfrac=anfrac,
sample=sample,
xicmmu=50,
type="DIA")
for jsonfile in glob.glob(dirname + '/*.json'):
# spectra = os.path.split(os.path.split(jsonfile)[0])[1]
data = json.loads(open(jsonfile).read())
rt = data['rt']
nrt = data.get('nrt')
trans = []
for s in data['series']:
trid = s['name'].split('/')[-2]
it = float(s['obs_relint']) / 10.0
if it <= 0:
continue
trans.append((trid, it))
trans.sort(key=lambda t: -t[1])
w = GPTWiki()
spectra2tg = defaultdict(set)
for tgpage in w.iterpages(include_categories=['TransitionGroup']):
tg = w.get(tgpage.name)
spectra = tg.get('spectra')
spectra2tg[spectra].add(tg.get('id'))
allspectra = set()
for transfile in sys.argv[1:]:
spectra, sample, method, index, extn = transfile.rsplit('.', 4)
spectra = os.path.split(spectra)[1]
allspectra.add(spectra)
w.addacquisition(name=spectra, method=method, sample=sample)
tgroup = defaultdict(dict)
for l in csv.DictReader(open(transfile), dialect='excel-tab'):
seq = l['PeptideSequence']
glyspec = l['Glycans']
modspec = l['Mods']
glycan = []
if glyspec != "-":
glycan = map(lambda t: (t[1], seq[int(t[0]) - 1] + str(t[0])),
map(lambda s: s.split(':'), glyspec.split(',')))
mods = []
if modspec != "-":
for mstr in modspec.split(','):
pos, delta = mstr.split(':')
delta, site, sym = mod_mw(float(delta), int(pos), seq)
mods.append((delta, site))
