def supporting_ppis(ppis, fnames, score_keys, sp_base, cutoff=0.5, verbose=True):
ppis_support = [pd.PairDict([]) for p in ppis]
eluts = [load_elution(f) for f in fnames]
for elut,skey in it.product(eluts, score_keys):
if verbose: print skey, ut.shortname(elut.filename)
od = orth.odict(sp_base, file_sp(elut.filename))
new_pairs = passing_pairs(elut, skey, cutoff)
for p,pdsupport in zip(ppis,ppis_support):
for opair in orth.orth_pairs(p[:2], od):
opair = tuple(opair)
if new_pairs.contains(opair):
pdsupport.set(opair,None)
return [list(p) + [s.d.keys()] for p,s in zip(ppis, ppis_support)]
def supporting_ppis(ppis, fnames, score_keys, sp_base, cutoff=0.5, verbose=True):
ppis_support = [pd.PairDict([]) for p in ppis]
eluts = [load_elution(f) for f in fnames]
for elut, skey in it.product(eluts, score_keys):
if verbose:
print skey, ut.shortname(elut.filename)
od = orth.odict(sp_base, file_sp(elut.filename))
new_pairs = passing_pairs(elut, skey, cutoff)
for p, pdsupport in zip(ppis, ppis_support):
for opair in orth.orth_pairs(p[:2], od):
opair = tuple(opair)
if new_pairs.contains(opair):
pdsupport.set(opair, None)
return [list(p) + [s.d.keys()] for p, s in zip(ppis, ppis_support)]
def supporting_ppis_separate(ppis, fnames, score_keys, sp_base, cutoff=0.5, verbose=True):
sps = set([file_sp(f) for f in fnames])
print "Species:", " ".join(sps)
ppis_support = [dict([(s, pd.PairDict([])) for s in sps]) for p in ppis]
eluts = [load_elution(f) for f in fnames]
for elut, skey in it.product(eluts, score_keys):
sp = file_sp(elut.filename)
if verbose:
print skey, ut.shortname(elut.filename)
od = orth.odict(sp_base, sp)
try:
new_pairs = passing_pairs(elut, skey, cutoff)
except IOError:
print "No file for %s %s" % (ut.shortname(elut.filename), skey)
continue
for p, dsupport in zip(ppis, ppis_support):
for opair in orth.orth_pairs(p[:2], od):
opair = tuple(opair)
if new_pairs.contains(opair):
dsupport[sp].set(opair, None)
return [list(p) + [[dsupport[sp].d.keys()] for sp in sps] for p, dsupport in zip(ppis, ppis_support)]
def supporting_ppis_separate(ppis, fnames, score_keys, sp_base, cutoff=0.5,
verbose=True):
sps = set([file_sp(f) for f in fnames])
print "Species:", ' '.join(sps)
ppis_support = [dict([(s, pd.PairDict([])) for s in sps]) for p in ppis]
eluts = [load_elution(f) for f in fnames]
for elut,skey in it.product(eluts, score_keys):
sp = file_sp(elut.filename)
if verbose: print skey, ut.shortname(elut.filename)
od = orth.odict(sp_base, sp)
try:
new_pairs = passing_pairs(elut, skey, cutoff)
except IOError:
print "No file for %s %s" % (ut.shortname(elut.filename), skey)
continue
for p,dsupport in zip(ppis,ppis_support):
for opair in orth.orth_pairs(p[:2], od):
opair = tuple(opair)
if new_pairs.contains(opair):
dsupport[sp].set(opair,None)
return [list(p) + [[dsupport[sp].d.keys()] for sp in sps]
for p,dsupport in zip(ppis, ppis_support)]
