def main():
parser = make_arg_parser()
args = parser.parse_args()
db = RefSeqDatabase()
nt = NCBITree()
# parse command line
with open(args.input, 'r') if args.input != '-' else sys.stdin as inf:
fasta_gen = FASTA(inf)
assembly_version = os.path.basename(args.input).split('_genomic')[0]
with open(args.output, 'w') if args.output != '-' else sys.stdout as outf:
for header, sequence in fasta_gen.read():
if '.cluster' in header:
header = header.replace('.cluster','_cluster')
else:
pass
ncbi_tid = db.get_ncbi_tid_from_refseq_accession_version(header.split('_cluster')[0])
if ncbi_tid:
ncbi_tid = ncbi_tid[0]
organism = nt.gg_lineage(ncbi_tid)
genus_species = organism.split(';')[-1]
genus_species = genus_species.replace('s__','')
outf.write('>ncbi_tid|%d|ref|%s|organism|%s|\n' % (ncbi_tid, header, genus_species))
outf.write(sequence+'\n')
else:
outf.write('>ref|%s|\n' % (header))
outf.write(sequence+'\n')
def main():
parser = make_arg_parser()
args = parser.parse_args()
db = RefSeqDatabase()
nt = NCBITree()
# parse command line
with open(args.input, 'r') if args.input != '-' else sys.stdin as inf:
fasta_gen = FASTA(inf)
assembly_version = os.path.basename(args.input).split('_genomic')[0]
with open(args.output, 'w') if args.output != '-' else sys.stdout as outf:
for header, sequence in fasta_gen.read():
if '.cluster' in header:
header = header.replace('.cluster','_cluster')
else:
pass
ncbi_tid = db.get_ncbi_tid_from_refseq_accession_version(header.split('_cluster')[0])
if ncbi_tid:
ncbi_tid = ncbi_tid[0]
organism = nt.gg_lineage(ncbi_tid)
# genus_species = organism.split(';')[-1]
# genus_species = genus_species.replace('s__','')
outf.write('>ncbi_tid|%d|ref|%s|organism|%s|\n' % (ncbi_tid, header, organism))
outf.write(sequence+'\n')
else:
outf.write('>ref|%s|\n' % (header))
outf.write(sequence+'\n')
