def test_run(self): """listdict initialization""" d = {"a": 1, "b": 2} ld = util.listdict(d) ld["a"].append(2) self.assertTrue(ld["a"] == [1, 2]) self.assertTrue(ld["b"] == [2])
def test_run(self): """listdict initialization""" d = {'a': 1, 'b': 2} ld = util.listdict(d) ld['a'].append(2) self.assertTrue(ld['a'] == [1, 2]) self.assertTrue(ld['b'] == [2])
def test_run(self): """listdict""" ld = util.listdict() ld["a"].append(1) ld["a"].append(2) self.assertTrue(ld["a"] == [1, 2])
def test_run(self): """listdict""" ld = util.listdict() ld['a'].append(1) ld['a'].append(2) self.assertTrue(ld['a'] == [1, 2])
query_keys = [] if not options.query_orf is []: # Specific ORF(s) query_keys += options.query_orf if not options.query_gene is []: # Specific gene(s) query_keys += [gene_orf_dict[k] for k in options.query_gene] # if k.startswith(options.query_gene)]) if len(query_keys) == 0: # Go through all proteins in database query_keys = all_keys # Load domain/color boundaries if not os.path.isfile(options.in_domain_fname): raise IOError("# Error: file {} does not exist".format(options.in_domain_fname)) dlr = util.DelimitedLineReader(file(options.in_domain_fname, 'r'), header=True) domain_boundaries = util.listdict() domain_colors = util.listdict() for flds in dlr.dictentries: orf = flds['orf'] score = flds['p.value'] #if orf in query_keys: # print orf, score, flds['start'], flds['end'], flds['sequence'] if score < options.score_threshold: domain_boundaries[orf].append((flds['start'], flds['end'])) domain_colors[orf].append(flds['color'].replace("0x","#")) # Remove gaps? if options.degap: for k in query_keys: prot_dict[k] = prot_dict[k].replace("-",'')
query_keys += options.query_orf if not options.query_gene is []: # Specific gene(s) query_keys += [gene_orf_dict[k] for k in options.query_gene ] # if k.startswith(options.query_gene)]) if len(query_keys) == 0: # Go through all proteins in database query_keys = all_keys # Load domain/color boundaries if not os.path.isfile(options.in_domain_fname): raise IOError("# Error: file {} does not exist".format( options.in_domain_fname)) dlr = util.DelimitedLineReader(file(options.in_domain_fname, 'r'), header=True) domain_boundaries = util.listdict() domain_colors = util.listdict() for flds in dlr.dictentries: orf = flds['orf'] score = flds['p.value'] #if orf in query_keys: # print orf, score, flds['start'], flds['end'], flds['sequence'] if score < options.score_threshold: domain_boundaries[orf].append((flds['start'], flds['end'])) domain_colors[orf].append(flds['color'].replace("0x", "#")) # Remove gaps? if options.degap: for k in query_keys: prot_dict[k] = prot_dict[k].replace("-", '')