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)
def run(record: Record, single_entry: bool, options: ConfigType) -> None:
""" The entry point of gff_parser.
Generates new features and adds them to the provided record.
Arguments:
record: the secmet.Record instance to alter
single_entry: if True, record and GFF ids must match
options: an antismash.Config object, used only for fetching the GFF path
Returns:
None
"""
# If there's only one sequence in both, read all, otherwise, read only appropriate part of GFF3.
limit_info = False # type: Union[bool, Dict[str, List[str]]]
if not single_entry:
limit_info = {'gff_id': [record.id]}
with open(options.genefinding_gff3) as handle:
features = get_features_from_file(record, handle, limit_info)
for feature in features:
try:
record.add_biopython_feature(feature)
except SecmetInvalidInputError as err:
raise AntismashInputError from err