def write_outputs(results: serialiser.AntismashResults,
options: ConfigType) -> None:
""" Write output files (webpage, genbank files, etc) to the output directory
Arguments:
results: a serialiser.AntismashResults instance
options: an antismash Config instance
Returns:
None
"""
# don't use results for which the module no longer exists to regenerate/calculate
module_results_per_record = []
for record_results in results.results:
record_result = {}
for module_name, result in record_results.items():
if isinstance(result, ModuleResults):
record_result[module_name] = result
module_results_per_record.append(record_result)
logging.debug("Creating results page")
html.write(results.records, module_results_per_record, options)
logging.debug("Creating results SVGs")
svg.write(options, module_results_per_record)
# convert records to biopython
bio_records = [record.to_biopython() for record in results.records]
# add antismash meta-annotation to records
add_antismash_comments(list(zip(results.records, bio_records)), options)
logging.debug("Writing cluster-specific genbank files")
for record, bio_record in zip(results.records, bio_records):
for region in record.get_regions():
region.write_to_genbank(directory=options.output_dir,
record=bio_record)
# write records to an aggregate output
base_filename = os.path.splitext(
os.path.join(options.output_dir, results.input_file))[0]
combined_filename = base_filename + ".gbk"
logging.debug("Writing final genbank file to '%s'", combined_filename)
SeqIO.write(bio_records, combined_filename, "genbank")
zipfile = base_filename + ".zip"
if os.path.exists(zipfile):
os.remove(zipfile)
if not options.skip_zip_file:
logging.debug("Zipping output to '%s'", zipfile)
with tempfile.NamedTemporaryFile(prefix="as_zip_tmp",
suffix=".zip") as temp:
shutil.make_archive(temp.name.replace(".zip", ""),
"zip",
root_dir=options.output_dir)
shutil.copy(temp.name, zipfile)
assert os.path.exists(zipfile)
def write_outputs(results, options) -> None:
""" Write output files (webpage, genbank files, etc) to the output directory
Arguments:
results: a serialiser.AntismashResults instance
options: an antismash Config instance
Returns:
None
"""
logging.debug("Creating results page")
html.write(results.records, results.results, options)
logging.debug("Creating results SVGs")
svg.write(options, results.results)
# convert records to biopython
bio_records = [record.to_biopython() for record in results.records]
logging.debug("Writing cluster-specific genbank files")
for record, bio_record in zip(results.records, bio_records):
for cluster in record.get_clusters():
cluster.write_to_genbank(directory=options.output_dir,
record=bio_record)
# write records to an aggregate output
base_filename = os.path.splitext(
os.path.join(options.output_dir, results.input_file))[0]
combined_filename = base_filename + ".gbk"
logging.debug("Writing final genbank file to '%s'", combined_filename)
SeqIO.write(bio_records, combined_filename, "genbank")
zipfile = base_filename + ".zip"
logging.debug("Zipping output to '%s'", zipfile)
if os.path.exists(zipfile):
os.remove(zipfile)
with tempfile.NamedTemporaryFile(prefix="as_zip_tmp",
suffix=".zip") as temp:
shutil.make_archive(temp.name.replace(".zip", ""),
"zip",
root_dir=options.output_dir)
shutil.copy(temp.name, zipfile)
assert os.path.exists(zipfile)
