def load_seq_pairs(fname, metab_exclude=None):
"""
metab_exclude: should be in sequential_metab/metabolites_exclude.txt
"""
S, entrez_enzymes, rnames, mnames = load_metabolic_data(fname)
ez2en = ut.dict_inverse_sets(orth.convert_dict('Hs','Hs_entrez'))
if metab_exclude:
print "Excluding %s metabolites, filtering rxns" % len(metab_exclude)
S, entrez_enzymes = filter_rxns_metabs(S, entrez_enzymes, rnames,
mnames, metab_exclude)
else:
print "No filtering of metabolites and rxns."
sequentials = seq_pairs(S, entrez_enzymes, conv_dict=ez2en)
return sequentials
def convdict_from_fname(species, ext_file):
# Doesn't yet work for the general case of possibly needing to go two
# steps--to the new species, then to a new seqdb
totype = '_'.join(ext_file.split('/')[-1].split('_')[:2]) #Hs_entrez;Dm_fbgn
# If there's no matching conversion file, assume it's not needed.
genedict = None
try:
genedict = orth.convert_dict(species, totype)
except IOError as e:
print 'No external conversion file:', species, totype, e.strerror
else:
if genedict is None:
print 'No external conversion file:', species, totype
else:
print 'Conversion file:', species, totype, len(genedict), 'keys'
return genedict
def load_kegg_sequentials(fname, do_convert=True):
dkegg = load_kegg_brite(fname)
kegg_paths = [ut.i1(v) for v in dkegg.values() if v]
def path_pairs(list_path):
return [(list_path[i],list_path[i+1]) for i in range(len(list_path)-1)]
group_pairs = ut.flatten([path_pairs(lpath) for lpath in kegg_paths])
#if return_groups:
#if conv_dict:
#return convert_groups_singles(labeled_pairs, conv_dict)
#else:
#return labeled_pairs
single_pairs = [(xi,yi) for x,y in group_pairs for xi in x for yi in y]
unique_pairs = pu.dedupe(single_pairs)
print "%s total, %s single, %s unique pairs returned" % (
len(group_pairs), len(single_pairs), len(unique_pairs))
if do_convert:
conv_dict = ut.dict_inverse_sets(orth.convert_dict('Hs','Hs_entrez'))
conv_pairs = convert_pairs_singles(unique_pairs, conv_dict)
print "%s converted pairs with 1-1 matches" % len(conv_pairs)
return conv_pairs
else:
return unique_pairs