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("-", '')
