def process_contig(self):
"""Process nuclotide sequence(s)."""
file_name = os.path.basename(self.input_sequence)
orf_obj = ORF(input_file=self.input_sequence, threads=self.threads, clean=self.clean, working_directory=self.working_directory, low_quality=self.low_quality, split_prodigal_jobs=self.split_prodigal_jobs)
orf_obj.contig_to_orf()
contig_fsa_file = os.path.join(self.working_directory,"{}.temp.contig.fsa".format(file_name))
blast_results_xml_file = os.path.join(self.working_directory,"{}.temp.contig.fsa.blastRes.xml".format(file_name))
try:
if os.stat(contig_fsa_file).st_size > 0:
logger.info("work with file {}".format(contig_fsa_file))
if self.aligner == "diamond":
diamond_obj = Diamond(contig_fsa_file, local_database=self.local_database, num_threads=self.threads)
diamond_obj.run()
else:
blast_obj = Blast(contig_fsa_file, local_database=self.local_database, num_threads=self.threads)
blast_obj.run()
self.set_xml_filepath(blast_results_xml_file)
else:
self.write_stub_output_file()
logger.error("no open reading frames (orfs) found.")
except Exception as e:
self.write_stub_output_file()
logger.exception("failed to write orf file")
else:
# logger.info("success procession orf file")
pass
def blast_reference_to_db_query(self, db, xml_file):
logger.info("blast_reference_to_db_query")
# blast all rrna db against query db
rrna_db_fasta = os.path.join(self.rgi_obj.db, "rnadb.fsa")
blast_obj = Blast(rrna_db_fasta,
program='blastn',
output_file=xml_file,
local_database=self.rgi_obj.local_database)
blast_obj.run_custom(db)
def process_protein(self):
"""Process protein sequence(s)."""
file_name = os.path.basename(self.input_sequence)
xml_file = os.path.join(self.working_directory,"{}.temp.blastRes.xml".format(file_name))
if self.aligner == "diamond":
diamond_obj = Diamond(self.input_sequence, xml_file, local_database=self.local_database, num_threads=self.threads)
diamond_obj.run()
else:
blast_obj = Blast(self.input_sequence, xml_file, local_database=self.local_database, num_threads=self.threads)
blast_obj.run()
self.set_xml_filepath(xml_file)