def tblastn(input_fasta, blastdb, min_ident, min_covs, evalue, out_dir, blast_results_file, logging, num_threads=1,
min_covhsp=25, seq_id_file=None):
blast_runner = BlastRunner(input_fasta, out_dir)
blast_runner.run_tblastn(query_fasta_path=input_fasta, blast_task='megablast', db_path=blastdb,
db_type='protein', min_cov=min_covs, min_ident=min_ident, evalue=evalue,
blast_outfile=blast_results_file,
num_threads=num_threads, seq_id_file=seq_id_file, logging=logging)
if os.path.getsize(blast_results_file) == 0:
os.remove(blast_results_file)
return False
blast_df = BlastReader(blast_results_file, logging).df
blast_df = blast_df.loc[blast_df['pident'] >= min_ident]
blast_df = blast_df.loc[blast_df['qcovs'] >= min_covs]
blast_df = blast_df.loc[blast_df['qcovhsp'] >= min_covhsp]
blast_df = blast_df.loc[blast_df['evalue'] <= evalue]
blast_df = fixStart(blast_df)
blast_df = blast_df.sort_values(['sseqid', 'sstart', 'send', 'bitscore'], ascending=[True, True, True, False])
blast_df = blast_df.reset_index(drop=True)
blast_df.to_csv(blast_results_file, sep='\t', header=True, line_terminator='\n', index=False)
return True
def mob_blast(input_fasta,
ref_db,
min_ident,
min_cov,
evalue,
tmp_dir,
blast_results_file,
overlap=5,
num_threads=1):
num_threads = 1
blast_runner = BlastRunner(input_fasta, tmp_dir)
blast_runner.makeblastdb(ref_db, 'nucl')
blast_runner.run_tblastn(query_fasta_path=input_fasta,
blast_task='megablast',
db_path=ref_db,
db_type='nucl',
min_cov=min_cov,
min_ident=min_ident,
evalue=evalue,
blast_outfile=blast_results_file,
num_threads=num_threads)
if os.path.getsize(blast_results_file) == 0:
return dict()
blast_df = BlastReader(blast_results_file).df
blast_df = blast_df.loc[blast_df['pident'] >= min_ident]
blast_df = blast_df.loc[blast_df['qcovs'] >= min_cov]
blast_df = blast_df.loc[blast_df['qcovhsp'] >= 25]
blast_df = fixStart(blast_df)
blast_df = blast_df.sort_values(['sseqid', 'sstart', 'send', 'bitscore'],
ascending=[True, True, True, False])
blast_df = blast_df.reset_index(drop=True)
blast_df = filter_overlaping_records(blast_df, overlap, 'sseqid', 'sstart',
'send', 'bitscore')
prev_size = 0
size = str(len(blast_df))
while size != prev_size:
blast_df = filter_overlaping_records(blast_df, overlap, 'sseqid',
'sstart', 'send', 'bitscore')
prev_size = size
size = str(len(blast_df))
#print(blast_df)
return blast_df
