def main(argv):
d2l = getlims()
d2t = gettargets()
excerpt = '/Users/berriz/Work/scratch/excerpt.tsv'
header, rows = rt.readtable(excerpt, headerrow=0)
sigclass = co.namedtuple('sigclass', header[1:], rename=True)
flds = set(si.SignatureData._fields)
t2s = dict()
rn.seed(0)
for row in sorted(rows):
drug, vv = row[0], row[1:]
if drug not in d2t:
continue
rangetested = d2l[drug]
signature = tuple(convert_conc_row(vv))
isclinical = rn.random() < ISCLINICAL_CUTOFF
isselective = rn.random() < ISSELECTIVE_CUTOFF
isprimary = rn.random() < ISPRIMARY_CUTOFF
data = si.SignatureData(**(sd.superdict(locals()).subdict(flds)))
for t in d2t[drug]:
t2s.setdefault(t, []).append(data)
for vv in t2s.values():
drugs = set(v.drug for v in vv)
assert len(drugs) == len(vv)
print ' LATEST =',
pp.pprint(t2s)
def main(argv):
d2l = getlims()
d2t = gettargets()
excerpt = '/Users/berriz/Work/scratch/excerpt.tsv'
header, rows = rt.readtable(excerpt, headerrow=0)
sigclass = co.namedtuple('sigclass', header[1:], rename=True)
flds = set(si.SignatureData._fields)
t2s = dict()
rn.seed(0)
for row in sorted(rows):
drug, vv = row[0], row[1:]
if drug not in d2t:
continue
rangetested = d2l[drug]
signature = tuple(convert_conc_row(vv))
isclinical = rn.random() < ISCLINICAL_CUTOFF
isselective = rn.random() < ISSELECTIVE_CUTOFF
isprimary = rn.random() < ISPRIMARY_CUTOFF
data = si.SignatureData(**(sd.superdict(locals()).subdict(flds)))
for t in d2t[drug]:
t2s.setdefault(t, []).append(data)
for vv in t2s.values():
drugs = set(v.drug for v in vv)
assert len(drugs) == len(vv)
print ' LATEST =',
pp.pprint(t2s)
def gettargets():
tgts = '/Users/berriz/Work/attachments/MF/LBNL_Gray_drug_targets_encoded_10Feb.txt'
_, rows = rt.readtable(tgts, headerrow=0)
comma_split_re = re.compile(r'\s*,\s*')
d2t = dict()
for drug, info in rows:
d2t.setdefault(drug, []).extend(comma_split_re.split(info))
return d2t
def gettargets():
tgts = '/Users/berriz/Work/attachments/MF/LBNL_Gray_drug_targets_encoded_10Feb.txt'
_, rows = rt.readtable(tgts, headerrow=0)
comma_split_re = re.compile(r'\s*,\s*')
d2t = dict()
for drug, info in rows:
d2t.setdefault(drug, []).extend(comma_split_re.split(info))
return d2t
def getlims():
gi50 = '/Users/berriz/Work/scratch/gi50.tsv'
header, namedrows = rt.readtable(gi50, headerrow=0)
rows = tuple(convert_conc_row(nr[1:]) for nr in namedrows)
cols = zip(*rows)
errors = []
def resolve(rng, candidates):
assert rng[0] <= rng[1]
found = []
garbage = []
puramierda = []
for pl in candidates:
if pl[0] <= rng[0] and rng[1] <= pl[1]:
found.append(pl)
elif pl[0] == rng[0] or rng[1] == pl[1]:
garbage.append(pl)
elif pl[0] < rng[0] or rng[1] < pl[1]:
puramierda.append(pl)
lfound = len(found)
if lfound == 1:
return found[0]
if lfound == 0:
lgarbage = len(garbage)
if lgarbage == 1:
errors.append('found garbage for %s %s' % (drug, rng))
toshow = garbage
ret = garbage[0]
else:
if lgarbage > 1 or len(puramierda):
errors.append('found PURA MIERDA for %s %s' % (drug, rng))
toshow = garbage + puramierda
else:
errors.append('no dice for %s %s' % (drug, rng))
toshow = candidates
ret = None
elif lfound > 1:
found2 = []
for pl in found:
if ((pl[0] == rng[0] <= rng[1])
or (rng[0] <= rng[1] == pl[1])):
found2.append(pl)
if len(found2) == 1:
ret = found2[0]
else:
(_, imin) = mm.minmax((t[1] - t[0] for t in found),
warg=True)[0]
ret = found[imin]
errors.append('too many dice for %s %s:' % (drug, rng))
toshow = found
for t in toshow:
errors.append(' %s' % (t, ))
errors.append('')
return ret
d2l = dict()
pls = possible_lims()
for drug, col in zip(header[1:], cols):
rng = lims(col)
d2l[drug] = resolve(rng, pls[drug])
if errors:
print
for e in errors:
print e
return d2l
def getlims():
gi50 = '/Users/berriz/Work/scratch/gi50.tsv'
header, namedrows = rt.readtable(gi50, headerrow=0)
rows = tuple(convert_conc_row(nr[1:]) for nr in namedrows)
cols = zip(*rows)
errors = []
def resolve(rng, candidates):
assert rng[0] <= rng[1]
found = []
garbage = []
puramierda = []
for pl in candidates:
if pl[0] <= rng[0] and rng[1] <= pl[1]:
found.append(pl)
elif pl[0] == rng[0] or rng[1] == pl[1]:
garbage.append(pl)
elif pl[0] < rng[0] or rng[1] < pl[1]:
puramierda.append(pl)
lfound = len(found)
if lfound == 1:
return found[0]
if lfound == 0:
lgarbage = len(garbage)
if lgarbage == 1:
errors.append('found garbage for %s %s' % (drug, rng))
toshow = garbage
ret = garbage[0]
else:
if lgarbage > 1 or len(puramierda):
errors.append('found PURA MIERDA for %s %s' % (drug, rng))
toshow = garbage + puramierda
else:
errors.append('no dice for %s %s' % (drug, rng))
toshow = candidates
ret = None
elif lfound > 1:
found2 = []
for pl in found:
if ((pl[0] == rng[0] <= rng[1]) or
(rng[0] <= rng[1] == pl[1])):
found2.append(pl)
if len(found2) == 1:
ret = found2[0]
else:
(_, imin) = mm.minmax((t[1]-t[0] for t in found), warg=True)[0]
ret = found[imin]
errors.append('too many dice for %s %s:' % (drug, rng))
toshow = found
for t in toshow:
errors.append(' %s' % (t,))
errors.append('')
return ret
d2l = dict()
pls = possible_lims()
for drug, col in zip(header[1:], cols):
rng = lims(col)
d2l[drug] = resolve(rng, pls[drug])
if errors:
print
for e in errors:
print e
return d2l
