def process_contig(self):
"""Process nuclotide sequence(s)."""
file_name = os.path.basename(self.input_sequence)
output = self.output_file
tax_class = self.tax_class
print("OKOKOKOKOKOK")
orf_obj = ORF(input_file=self.input_sequence)
orf_obj.contig_to_orf()
contig_fsa_file = os.path.join(self.working_directory,
"{}.temp.contig.fsa".format(file_name))
try:
if os.stat(contig_fsa_file).st_size > 0:
if self.aligner == "diamond":
diamond_obj = Diamond(input_file=contig_fsa_file,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
diamond_obj.run()
else:
print(contig_fsa_file)
blast_obj = Blast(input_file=contig_fsa_file,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
blast_obj.run()
else:
self.write_stub_output_file()
except Exception as e:
pass
else:
pass
def process_protein(self):
"""Process protein sequence(s)."""
file_name = os.path.basename(self.input_sequence)
output = self.output_file
tax_class = self.tax_class
if self.aligner == "diamond":
diamond_obj = Diamond(self.input_sequence,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
diamond_obj.run()
else:
blast_obj = Blast(input_file=file_name,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
blast_obj.run()
