def genes2phens(p2entrez_file, e2z=None):
ensg2z = e2z if e2z else ut.load_dict_sets(ut.proj_path('convert', 'Hs2Hs_entrez.tab'))
def dict_sets_rem_prefix(d, sep):
d = dict([(k,set([vi.split(sep)[1] for vi in v])) for k,v in d.items()])
return d
p2z = dict_sets_rem_prefix(ut.load_dict_sets(p2entrez_file), ":")
return ut.compose_dict_sets(ensg2z, ut.dict_inverse_sets(p2z))
def custom_conversion(fromtype, totype):
"""
Check for a custom file in data/convert
Return None if not found.
"""
fname = "%s2%s.tab" % (fromtype, totype)
fpath = ut.proj_path('convert',fname)
if os.path.exists(fpath):
return ut.load_dict_sets(fpath)
def custom_conversion(fromtype, totype):
"""
Check for a custom file in data/convert
Return None if not found.
"""
fname = "%s2%s.tab" % (fromtype, totype)
fpath = ut.proj_path('convert', fname)
if os.path.exists(fpath):
return ut.load_dict_sets(fpath)
def load_havug_cxs(convert_ensg=True):
fname = ut.proj_path('havug_cxs')
u2e = ut.dict_inverse_sets(ut.load_dict_sets(
'../../data/convert/Hs2Hs_uni.tab'))
hcxs = ut.load_list_of_type(fname,set)
if convert_ensg:
hcxs = convert_complexes([(i,c) for i,c in
enumerate(hcxs)], u2e,
seqs.load_prots_from_fasta('../../data/sequences/canon/Hs.fasta'))
return hcxs
def load_havug_ppis():
hints = ut.load_list_of_lists('../../docs/SupplementaryTableS2.tab')
u2e = ut.dict_inverse_sets(ut.load_dict_sets('../../data/convert/Hs2Hs_uni.tab'))
hints = [[list(u2e.get(p,['NoTranslation']))[0] for p in c[:2]]+[c[2]] for c in hints]
return hints
