def __init__(self, sp='Hs'):
lines = ut.load_list_of_lists(ut.proj_path('gene_desc_'+sp))[1:]
processed = [tuple([l[0],l[1].lower()] + (l[2:] if len(l)>2 else [''])) for l in
lines if len(l)>1]
self.gnames = [(l[1], l[2].split('[')[0]) for l in processed]
self.name2id = dict(((l[1],l[0]) for l in processed))
self.id2name = dict(((l[0], l[1]) for l in processed))
self.name2desc = dict(self.gnames)
self.id2desc = dict(((l[0],l[2].split('[')[0]) for l in processed))
self.id2all = dict(((l[0],l[1:]) for l in processed))
def write_prot_counts(f_peplist, only_uniques, f_pep2prots=None):
if f_peplist.find('pep_count_') > -1:
peplist = peplist_from_pepcount(f_peplist)
else:
peplist = ut.load_list_of_lists(f_peplist)
if f_pep2prots:
pep2prots = load_pep2prots(f_pep2prots)
prots, samples, counts, totals = prot_counts_pep2prots(peplist,
only_uniques, pep2prots)
else:
prots, samples, counts, totals = prot_counts(peplist, only_uniques)
suffix = 'prot_count' + ('_uniqpeps2' if only_uniques else '')
fname_out = f_peplist.replace('pep_list',suffix).replace('pep_count',suffix)
f_counts = open(fname_out, 'w')
f_counts.write("#ProtID\tTotalCount\t%s\n"%('\t'.join(samples)))
for i,prot in enumerate(prots):
out_str = ['%0.2f' % count for count in counts[i,:]]
f_counts.write("%s\t%.2f\t%s\n"%(prot, totals[i], '\t'.join(out_str)))
f_counts.close()
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
def read_mcl_output(fname):
cxs = [set(c) for c in ut.load_list_of_lists(fname)]
return cxs
