Fixed issue related to CDS counting when it is not possible to predic…

…t CDSs for one or more inputs.

CHEWBBACA/AlleleCall/allele_call.py

@@ -1990,9 +1990,9 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 			print('Make sure that Pyrodigal runs in meta mode (--pm meta) '
 				  'if any input file has less than 100kbp.')
 		if len(cds_fastas) == 0:
-			sys.exit(f'\n{ct.CANNOT_PREDICT}')
+			sys.exit(f'{ct.CANNOT_PREDICT}')
 
-		print(f'\nExtracted a total of {total_extracted} CDSs from {len(fasta_files)} inputs.')
+		print(f'\nExtracted a total of {total_extracted} CDSs from {len(fasta_files)-len(failed)} inputs.')
 	# Inputs are Fasta files with the predicted CDSs
 	else:
 		# Rename the CDSs in each file based on the input unique identifiers
@@ -2042,7 +2042,7 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
 	template_dict['int_to_unique'] = int_to_unique
 
 	# Change to unique integer identifiers
-	cds_counts = {unique_to_int[k]: v for k, v in cds_counts.items()}
+	cds_counts = {unique_to_int[k]: v for k, v in cds_counts.items() if k in unique_to_int}
 	template_dict['cds_counts'] = cds_counts
 
 	# Concatenate subgroups of FASTA files before deduplication

CHEWBBACA/utils/constants.py

@@ -528,7 +528,7 @@
 # e.g. files only contain sequence headers, contain invalid
 # sequences/chars or pyrodigal cannot predict any genes
 CANNOT_PREDICT = ('Could not predict CDSs from any of the input files.'
-				  '\nPlease provide input files in the accepted FASTA format.')
+				  '\nPlease verify the format of the input files.')
 
 INVALID_BSR = ('\nBSR value is not contained in the [0.0, 1.0] interval.')
 INVALID_BSR_TYPE = ('\nInvalid BSR value of {0}. BSR value must be contained in the [0.0, 1.0] interval.')