def _get_from_card(self, outprefix):
outprefix = os.path.abspath(outprefix)
tmpdir = outprefix + '.download'
current_dir = os.getcwd()
try:
os.mkdir(tmpdir)
os.chdir(tmpdir)
except:
raise Error('Error mkdir/chdir ' + tmpdir)
versions = self._get_card_versions('download.html')
if self.version is not None:
key = tuple([int(x) for x in self.version.split('.')])
if key not in versions:
raise Error('Error! Did not find requested version ' +
self.version)
else:
key = sorted(list(versions.keys()))[-1]
self.version = '.'.join([str(x) for x in key])
print('Getting version', self.version)
card_tarball_url = versions[key]
card_tarball = 'card.tar.bz2'
print('Working in temporary directory', tmpdir)
print('Downloading data from card:', card_tarball_url, flush=True)
common.syscall('wget -O ' + card_tarball + ' ' + card_tarball_url,
verbose=True)
print('...finished downloading', flush=True)
if not tarfile.is_tarfile(card_tarball):
raise Error(
'File ' + card_tarball + ' downloaded from ' +
card_tarball_url +
' does not look like a valid tar archive. Cannot continue')
json_file = './card.json'
with tarfile.open(card_tarball, 'r') as tfile:
tfile.extract(json_file)
print('Extracted json data file ',
json_file,
'. Reading its contents...',
sep='')
final_fasta = outprefix + '.fa'
final_tsv = outprefix + '.tsv'
log_file = outprefix + '.log'
f_out_fa = pyfastaq.utils.open_file_write(final_fasta)
f_out_tsv = pyfastaq.utils.open_file_write(final_tsv)
f_out_log = pyfastaq.utils.open_file_write(log_file)
with open(json_file) as f:
json_data = json.load(f)
json_data = {
int(x): json_data[x]
for x in json_data if not x.startswith('_')
}
print('Found',
len(json_data),
'records in the json file. Analysing...',
flush=True)
for gene_key, gene_dict in sorted(json_data.items()):
crecord = card_record.CardRecord(gene_dict)
data = crecord.get_data()
data['ARO_description'] = data['ARO_description'].encode('utf-8')
fasta_name_prefix = '.'.join([
card_record.CardRecord._ARO_name_to_fasta_name(
data['ARO_name']),
data['ARO_accession'],
])
for card_key, gi, genbank_id, start, end, dna_seq, protein_seq in data[
'dna_seqs_and_ids']:
if dna_seq == '':
print('Empty dna sequence',
gene_key,
data['ARO_id'],
data['ARO_accession'],
sep='\t',
file=f_out_log)
continue
fasta_id = '.'.join([
fasta_name_prefix, genbank_id, start + '-' + end, card_key
])
fasta = pyfastaq.sequences.Fasta(fasta_id, dna_seq)
if gi != 'NA':
gene_tuple = fasta.make_into_gene()
if gene_tuple is None:
print('Could not make gene from sequence',
fasta.id,
sep='\t',
file=f_out_log)
continue
else:
translated = gene_tuple[0].translate()
if gene_tuple[0][:3] in pyfastaq.genetic_codes.starts[
self.genetic_code]:
translated.seq = 'M' + translated.seq[1:]
if translated.seq[:-1] != protein_seq:
print(
'Translation of inferred gene dna sequence does not match protein sequence',
fasta.id,
sep='\t',
file=f_out_log)
continue
print(fasta, file=f_out_fa)
if gi == 'NA':
gene_or_not = '0'
variant_only = '0'
elif len(data['snps']) == 0:
gene_or_not = '1'
variant_only = '0'
else:
gene_or_not = '1'
variant_only = '1'
print(fasta.id,
gene_or_not,
variant_only,
'.',
'.',
data['ARO_name'],
sep='\t',
file=f_out_tsv)
if len(data['snps']) == 0 and data['ARO_description'] != '':
print(fasta.id,
gene_or_not,
variant_only,
'.',
'.',
data['ARO_description'],
sep='\t',
file=f_out_tsv)
else:
for snp in data['snps']:
if data['ARO_description'] != '':
print(fasta.id,
gene_or_not,
variant_only,
snp,
'.',
data['ARO_description'],
sep='\t',
file=f_out_tsv)
pyfastaq.utils.close(f_out_fa)
pyfastaq.utils.close(f_out_tsv)
pyfastaq.utils.close(f_out_log)
os.chdir(current_dir)
if not self.debug:
common.rmtree(tmpdir)
print('Extracted data and written ARIBA input files\n')
print('Finished. Final files are:',
final_fasta,
final_tsv,
sep='\n\t',
end='\n\n')
print('You can use them with ARIBA like this:')
print('ariba prepareref -f', final_fasta, '-m', final_tsv,
'output_directory\n')
print('If you use this downloaded data, please cite:')
print(
'"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database", Alcock et al 2020, PMID: 31665441'
)
print('and in your methods say that version', self.version,
'of the database was used')
def test_get_data(self):
d = {
'ARO_id': '123',
'ARO_accession': '1234567',
'ARO_name': 'ARO_name1',
'ARO_description': 'ARO description that we want.',
'model_id': '1',
'model_name': 'Model_name1',
'model_type': 'protein homolog model',
'model_type_id': '12345',
'model_description': 'Models to detect proteins conferring antibiotic resistance, which include a reference protein sequence and a curated BLASTP cut-off.',
'model_sequences': {
'sequence': {
'1234': {
'protein_sequence': {
'sequence': 'MCDE*',
'GI': '229597524'
},
'dna_sequence': {
'sequence': 'ATGTGCGATGAATAA',
'strand': '+',
'fmax': '1194',
'fmin': '0',
'accession': 'XX0000001'
},
'NCBI_taxonomy': {
'NCBI_taxonomy_cvterm_id': '234567',
'NCBI_taxonomy_id': '42',
'NCBI_taxonomy_name': 'Genus1 species1'
}
}
}
},
'model_param': {
'blastp_evalue': {} # we're ignoring this, so make it empty for tests to save a few lines
},
'ARO_category': {
'36696': {
'category_aro_description': 'Enzyme that catalyzes the inactivation of an antibiotic resulting in resistance. Inactivation includes chemical modification, destruction, etc.',
'category_aro_cvterm_id': '36696',
'category_aro_accession': '3000557',
'category_aro_name': 'antibiotic inactivation enzyme'
},
'36268': {
'category_aro_description': 'Genes conferring resistance to beta-lactams.',
'category_aro_cvterm_id': '36268',
'category_aro_accession': '3000129',
'category_aro_name': 'beta-lactam resistance gene'
}
},
}
expected = {
'ARO_id': '123',
'ARO_accession': '1234567',
'ARO_name': 'ARO_name1',
'ARO_description': 'ARO description that we want.',
'dna_seqs_and_ids': [(
'1234',
'229597524',
'XX0000001',
'0',
'1194',
'ATGTGCGATGAATAA',
'MCDE*'
)],
'snps': set(),
}
record = card_record.CardRecord(d)
got = record.get_data()
self.assertEqual(expected, got)
d['model_param'] = {
'snp': {
'param_value': {
'1': 'I42L',
'2': 'S100T',
}
}
}
expected['snps'] = {'I42L', 'S100T'}
record = card_record.CardRecord(d)
got = record.get_data()
self.assertEqual(expected, got)
