Reverted changes related to blastdb_aliastool and BLAST v4 databases.…

… Using BLAST v5 databases.

CHEWBBACA/AlleleCall/allele_call.py

@@ -1749,7 +1749,8 @@ def create_missing_fasta(class_files, fasta_file, input_map, dna_hashtable,
 
 def select_representatives(representative_candidates, locus, fasta_file,
 						   iteration, output_directory, blastp_path,
-						   blast_db, blast_score_ratio, threads):
+						   blast_db, blast_score_ratio, threads,
+						   blastdb_aliastool_path):
 	"""Select new representative alleles for a locus.
 
 	Parameters
@@ -1774,6 +1775,9 @@ def select_representatives(representative_candidates, locus, fasta_file,
 		BLAST Score Ratio value.
 	threads : int
 		Number of threads passed to BLAST.
+	blastdb_aliastool_path : str or None
+		Path to the `blastdb_aliastool` executable used to convert
+		the list of seqids to binary format.
 
 	Returns
 	-------
@@ -1788,6 +1792,12 @@ def select_representatives(representative_candidates, locus, fasta_file,
 	ids_file = fo.join_paths(output_directory,
 							 ['{0}_candidates_ids_{1}.fasta'.format(locus, iteration)])
 	fo.write_lines(list(representative_candidates.keys()), ids_file)
+	# Convert to binary format if BLAST>=2.10
+	binary_file = f'{ids_file}.bin'
+	blastp_std = bw.run_blastdb_aliastool(blastdb_aliastool_path,
+											ids_file,
+											binary_file)
+	ids_file = binary_file
 
 	# BLASTp to compare all candidates
 	blast_output = fo.join_paths(output_directory,
@@ -2270,9 +2280,10 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 	clustering_dir = fo.join_paths(temp_directory, ['4_clustering'])
 	fo.create_directory(clustering_dir)
 
-	# Define BLASTp and makeblastdb paths
+	# Define BLASTp, makeblastdb and blastdb_aliastool paths
 	blastp_path = fo.join_paths(config['BLAST path'], [ct.BLASTP_ALIAS])
 	makeblastdb_path = fo.join_paths(config['BLAST path'], [ct.MAKEBLASTDB_ALIAS])
+	blastdb_aliastool_path = fo.join_paths(config['BLAST path'], [ct.BLASTDB_ALIASTOOL_ALIAS])
 
 	# Concatenate representative FASTA files
 	concat_reps = fo.join_paths(reps_protein_dir, ['loci_to_call_translated_representatives.fasta'])
@@ -2293,7 +2304,8 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 		self_scores = cf.determine_self_scores(concat_full_reps, self_score_dir,
 											   makeblastdb_path, blastp_path,
 											   'prot',
-											   config['CPU cores'])
+											   config['CPU cores'],
+											   blastdb_aliastool_path)
 		fo.pickle_dumper(self_scores, self_score_file)
 	else:
 		self_scores = fo.pickle_loader(self_score_file)
@@ -2347,6 +2359,7 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 															 clustering_dir, blastp_path,
 															 makeblastdb_path,
 															 config['CPU cores'],
+															 blastdb_aliastool_path
 															 True)
 
 		blast_files = im.flatten_list(blast_results)
@@ -2477,6 +2490,11 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 		# Create text file with unclassified seqids
 		remaining_seqids_file = fo.join_paths(iteration_directory, ['unclassified_seqids_{0}.txt'.format(iteration)])
 		fo.write_lines(unclassified_seqids, remaining_seqids_file)
+		binary_file = f'{remaining_seqids_file}.bin'
+		blastp_std = bw.run_blastdb_aliastool(blastdb_aliastool_path,
+												remaining_seqids_file,
+												binary_file)
+		remaining_seqids_file = binary_file
 
 		# BLAST representatives against unclassified sequences
 		# Iterative process until no more sequences are classified
@@ -2633,7 +2651,7 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 					representative_inputs.append([current_candidates, k, fasta_file,
 												  iteration, blast_selection_dir, blastp_path,
 												  blast_db, config['BLAST Score Ratio'], 1,
-												  select_representatives])
+												  blastdb_aliastool_path, select_representatives])
 				# Single candidate
 				else:
 					representatives[k] = [(v[0][1], v[0][3])]
@@ -2687,7 +2705,8 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 			fo.create_directory(candidates_blast_dir)
 			new_self_scores = cf.determine_self_scores(concat_repy, candidates_blast_dir,
 													   makeblastdb_path, blastp_path,
-													   'prot', config['CPU cores'])
+													   'prot', config['CPU cores'],
+													   blastdb_aliastool_path)
 
 			# This includes self-score for candidates that are not added
 			# (e.g. classification changes due to multiple matches)