def test_features_from_file(self):
filename = path.get_full_path(__file__, 'data',
'fumigatus.cluster1.gff')
features = gff_parser.get_features_from_file(open(filename))
assert len(features) == 11
for feature in features:
assert feature.type == 'CDS'
assert isinstance(feature.location, CompoundLocation)
def run_glimmerhmm(record: Record) -> None:
""" Run glimmerhmm on the record, parse the results and add all detected
genes to the record
"""
with TemporaryDirectory(change=True):
# Write FASTA file and run GlimmerHMM
fasta_file = write_search_fasta(record)
results_text = run_external(fasta_file)
handle = StringIO(results_text)
features = get_features_from_file(record, handle)
for feature in features:
record.add_biopython_feature(feature)
def run_glimmerhmm(record: Record) -> None:
""" Run glimmerhmm on the record, parse the results and add all detected
genes to the record
"""
with TemporaryDirectory(change=True):
# glimmerHMM/gff_parser handles some record names poorly (e.g. leading - or only '.')
orig_id = record.id
record.id = "input"
# Write FASTA file and run GlimmerHMM
fasta_file = write_search_fasta(record)
record.id = orig_id
results_text = run_external(fasta_file)
if not "CDS" in results_text:
return
handle = StringIO(results_text)
features = get_features_from_file(handle)["input"]
for feature in features:
record.add_biopython_feature(feature)