def main():
parser = argparse.ArgumentParser(description="Extract tRNA and rRNA features from a sequence specified by NCBI GenBank ID")
parser.add_argument("ncbi_id", help="NCBI GenBank ID to extract RNA features from.")
parser.add_argument("--reuse", action="store_true", default=False,
help="Reuse exising file if available")
args = parser.parse_args()
# Download file in GenBank format
# Could download into a StringIO buffer by using the
# ncbi_acc_download.download functions directly, but then we can't --reuse
filename = "{}.gbk".format(args.ncbi_id)
if not os.path.isfile(filename):
cfg = Config(recursive=True, format="genbank", out=filename)
download_to_file(args.ncbi_id, cfg, filename)
# Extract RNA features
records = list(SeqIO.parse(filename, "genbank"))
for record in records:
for feature in record.features:
if feature.type not in ("tRNA", "rRNA"):
continue
# this crashes if there is no locus tag, but NCBI genomes should have these
locus_tag = feature.qualifiers['locus_tag'][0]
header = ">{type}|{locus_tag}".format(type=feature.type, locus_tag=locus_tag)
seq = feature.extract(record.seq)
print(header, seq, sep='\n')
def test_download_to_file(req, tmpdir):
"""Test downloading things from NCBI."""
req.get(ENTREZ_URL, text='This works.')
outdir = tmpdir.mkdir('outdir')
filename = outdir.join('foo')
expected = outdir.join('foo.gbk')
config = core.Config(molecule='nucleotide', verbose=False)
core.download_to_file('FOO', config, filename=filename)
assert expected.check()
def download_job_files(config: Config, job: Job) -> None:
"""Download the files of an antiSMASH job."""
job.state = 'downloading'
job.status = "Downloading {} from NCBI".format(job.download)
job.trace.append(config.name)
job.commit()
dl_prefix = os.path.join(config.workdir, job.job_id, 'input', job.download)
nad_conf = NadConfig(format="genbank", recursive=True)
download_to_file(job.download, nad_conf, dl_prefix)
job.state = 'queued'
job.needs_download = False
job.status = "pending"
job.filename = '{}.gbk'.format(job.download)
job.commit()
def test_download_to_file_retry(req, tmpdir):
"""Test downloading things from NCBI, retrying after a 429 status."""
req.get(ENTREZ_URL,
response_list=[
{
"text": u'Whoa, slow down',
"status_code": 429,
"headers": {
"Retry-After": "0"
}
},
{
"text": 'This works.'
},
])
outdir = tmpdir.mkdir('outdir')
filename = outdir.join('foo')
expected = outdir.join('foo.gbk')
config = core.Config(molecule='nucleotide', verbose=False)
core.download_to_file('FOO', config, filename=filename)
assert expected.check()
def test_download_to_file_append(req, tmpdir):
"""Test appending multiple downloads into a single file."""
req.get(ENTREZ_URL, text='This works.\n')
outdir = tmpdir.mkdir('outdir')
filename = outdir.join('foo.txt')
expected = outdir.join('foo.txt')
config = core.Config(molecule='nucleotide', verbose=False, out='foo.txt')
core.download_to_file('FOO', config, filename=str(filename), append=False)
core.download_to_file('BAR', config, filename=str(filename), append=True)
core.download_to_file('BAZ', config, filename=str(filename), append=True)
assert expected.check()
assert len(expected.readlines()) == 3