def test_record_to_json_and_back(self):
filename = get_path_to_nisin_genbank()
records = list(seqio.parse(open(filename), "genbank"))
records = [
Record.from_biopython(rec, taxon="bacteria") for rec in records
]
rec_results = [{}, {}, {}]
results = serialiser.AntismashResults(filename, records, rec_results,
"dummy")
json_handle = StringIO()
results.write_to_file(json_handle)
json_handle.seek(0)
new_results = serialiser.AntismashResults.from_file(json_handle,
taxon="bacteria")
assert results.to_json() == new_results.to_json()
# check no records were lost
assert len(new_results.records) == len(results.records)
# check that the contents of the records is the same
# by converting to biopython and writing to genbanks
original = self.create_data_stream(results.records)
new = self.create_data_stream(new_results.records)
oldvalue = original.getvalue()
newvalue = new.getvalue()
with TemporaryDirectory(change=True):
open("old.json", "w").write(oldvalue)
open("new.json", "w").write(newvalue)
for oldline, newline in zip(oldvalue.split('\n'),
newvalue.split('\n')):
assert oldline == newline
def read_data(sequence_file, options) -> serialiser.AntismashResults:
""" Reads in the data to be used in the analysis run. Can be provided as
as a sequence file (fasta/genbank) or as file of prior results
Arguments:
sequence_file: A fasta/genbank file to read (or None)
options: An antismash Config instance
Returns:
a AntismashResults instance, populated only if reusing results
"""
if not sequence_file and not options.reuse_results:
raise ValueError("No sequence file or prior results to read")
if sequence_file:
records = record_processing.parse_input_sequence(
sequence_file, options.taxon, options.minlength, options.start,
options.end)
return serialiser.AntismashResults(
sequence_file.rsplit(os.sep, 1)[-1], records,
[{} for i in range(len(records))], __version__)
logging.debug("Attempting to reuse previous results in: %s",
options.reuse_results)
with open(options.reuse_results) as handle:
contents = handle.read()
if not contents:
raise ValueError("No results contained in file: %s" %
options.reuse_results)
results = serialiser.AntismashResults.from_file(options.reuse_results,
options.taxon)
return results
def read_data(sequence_file: Optional[str],
options: ConfigType) -> serialiser.AntismashResults:
""" Reads in the data to be used in the analysis run. Can be provided as
as a sequence file (fasta/genbank) or as file of prior results
Arguments:
sequence_file: A fasta/genbank file to read (or None)
options: An antismash Config instance
Returns:
a AntismashResults instance, populated only if reusing results
"""
if not sequence_file and not options.reuse_results:
raise ValueError("No sequence file or prior results to read")
if sequence_file:
records = record_processing.parse_input_sequence(
sequence_file,
options.taxon,
options.minlength,
options.start,
options.end,
gff_file=options.genefinding_gff3)
results = serialiser.AntismashResults(sequence_file.rsplit(os.sep,
1)[-1],
records, [{} for i in records],
__version__,
taxon=options.taxon)
update_config({"input_file": os.path.splitext(results.input_file)[1]})
else:
logging.debug("Attempting to reuse previous results in: %s",
options.reuse_results)
with open(options.reuse_results) as handle:
contents = handle.read()
if not contents:
raise ValueError("No results contained in file: %s" %
options.reuse_results)
results = serialiser.AntismashResults.from_file(options.reuse_results)
for record in results.records:
record.strip_antismash_annotations()
if options.taxon != results.taxon:
logging.info("Reusing taxon %s from prior results", results.taxon)
update_config({"taxon": results.taxon})
update_config({"input_file": os.path.splitext(results.input_file)[0]})
return results
