Fixed new allele count in AlleleCall stdout. Fixed issue #71.

CHEWBBACA/AlleleCall/allele_call.py

@@ -2762,7 +2762,7 @@ def main(input_file, loci_list, schema_directory, output_directory,
 
     # Get list of loci in the schema
     schema_loci = fo.pickle_loader(fo.join_paths(schema_directory,
-                                                 [ct.LOCI_LIST_FILE]))
+                                                 [ct.GENE_LIST_BASENAME]))
     schema_loci_paths = [fo.join_paths(schema_directory, [file])
                             for file in schema_loci]
 
@@ -2847,8 +2847,8 @@ def main(input_file, loci_list, schema_directory, output_directory,
                                               mo.function_helper,
                                               config['CPU cores'],
                                               show_progress=False)
-    novel_alleles_count = sum(len(v) for v in novel_alleles)
     novel_alleles = im.merge_dictionaries(novel_alleles)
+    novel_alleles_count = sum(len(v) for k, v in novel_alleles.items())
     print(f'Assigned identifiers to {novel_alleles_count} new alleles.')
 
     updated_files = {}
@@ -3009,9 +3009,9 @@ def main(input_file, loci_list, schema_directory, output_directory,
                                                      classification_labels)
 
     print(f'Classified a total of {total_cds} CDSs.')
-    class_counts_header = [f'{c:^8}' for c in ct.ALLELECALL_CLASSIFICATIONS]
+    class_counts_header = [f'{c:^8}' for c in ct.ALLELECALL_CLASSIFICATIONS[:-1]]
     class_counts_header = ' '.join(class_counts_header)
-    class_counts_values = [f'{global_counts.get(c, 0):^8}' for c in ct.ALLELECALL_CLASSIFICATIONS]
+    class_counts_values = [f'{global_counts.get(c, 0):^8}' for c in ct.ALLELECALL_CLASSIFICATIONS[:-1]]
     class_counts_values = ' '.join(class_counts_values)
     print('='*len(class_counts_header))
     print(class_counts_header)
@@ -3020,8 +3020,8 @@ def main(input_file, loci_list, schema_directory, output_directory,
     print('='*len(class_counts_header))
 
     if no_inferred is False and config['Mode'] != 1 and len(novel_alleles) > 0:
-        print('Added {0} novel alleles to the schema.'.format(sum(added2)))
-        print('Added {0} representative alleles to the schema.'.format(added[1]))
+        print('Added {0} new alleles to the schema.'.format(sum(added2)))
+        print('Added {0} new representative alleles to the schema.'.format(added[1]))
     elif no_inferred is True:
         print('User passed "--no-inferred". No alleles added to the schema.')
     elif len(novel_alleles) == 0:

CHEWBBACA/CHEWBBACA_NS/download_schema.py

@@ -531,18 +531,10 @@ def main(species_id, schema_id, download_folder, cpu_cores,
         fo.remove_files(ns_files)
 
         # Write hidden schema config file
-        del(schema_params_dict['Schema_lock'])
-        schema_config = pv.write_schema_config(schema_params_dict['bsr'],
-                                               ptf_hash,
-                                               schema_params_dict['translation_table'],
-                                               schema_params_dict['minimum_locus_length'],
+        schema_params_dict['ptf_path'] = ptf_hash
+        schema_params_dict['window_size'] = schema_params_dict.get('window_size', None)
+        schema_config = pv.write_schema_config(schema_params_dict,
                                                schema_params_dict['chewBBACA_version'],
-                                               schema_params_dict['size_threshold'],
-                                               schema_params_dict['word_size'],
-                                               schema_params_dict.get('window_size', None),  # add window size to chewie-NS
-                                               schema_params_dict['cluster_sim'],
-                                               schema_params_dict['representative_filter'],
-                                               schema_params_dict['intraCluster_filter'],
                                                schema_path)
 
         # Create ns_config file

CHEWBBACA/CHEWBBACA_NS/synchronize_schema.py

@@ -761,7 +761,7 @@ def main(schema_directory, cpu_cores, nomenclature_server,
     headers_post_bytes['Authorization'] = token
     headers_post_bytes['user_id'] = user_id
 
-    schema_params = pv.read_configs(schema_directory, '.schema_config')
+    schema_params = pv.read_configs(schema_directory, ct.SCHEMA_CONFIG_BASENAME)
 
     # verify that local configs have a single value per parameter
     if all([len(schema_params[k]) == 1
@@ -819,7 +819,7 @@ def main(schema_directory, cpu_cores, nomenclature_server,
           ''.format(count, len(loci_alleles)))
 
     # Get schema files from genes list file
-    genes_list = fo.join_paths(schema_directory, ['.genes_list'])
+    genes_list = fo.join_paths(schema_directory, [ct.GENE_LIST_BASENAME])
     genes = fo.pickle_loader(genes_list)
 
     # update loci structure

CHEWBBACA/CHEWBBACA_NS/upload_schema.py

@@ -969,7 +969,7 @@ def main(schema_directory, species_id, schema_name, loci_prefix,
     print('Local schema: {0}'.format(schema_directory))
 
     # Get schema files from genes list file
-    genes_list = os.path.join(schema_directory, '.genes_list')
+    genes_list = fo.join_paths(schema_directory, [ct.GENE_LIST_BASENAME])
     genes = fo.pickle_loader(genes_list)
     fasta_paths = [os.path.join(schema_directory, file) for file in genes]
     fasta_paths.sort()
@@ -993,7 +993,7 @@ def main(schema_directory, species_id, schema_name, loci_prefix,
     # Verify schema config
     print('Verifying schema configs...')
     # Load schema config file
-    configs = pv.read_configs(schema_directory, '.schema_config')
+    configs = pv.read_configs(schema_directory, ct.SCHEMA_CONFIG_BASENAME)
 
     # Validate arguments values
     schema_ptfs = configs['prodigal_training_file']

CHEWBBACA/SchemaEvaluator/evaluate_schema.py

@@ -577,7 +577,7 @@ def main(schema_directory, output_directory, genes_list, annotations,
                       for file in schema_files}
 
     # Check if the schema was created with chewBBACA
-    config_file = os.path.join(schema_directory, ".schema_config")
+    config_file = fo.join_paths(schema_directory, [ct.SCHEMA_CONFIG_BASENAME])
     if os.path.exists(config_file):
         # get the schema configs
         with open(config_file, "rb") as cf:

CHEWBBACA/UniprotFinder/annotate_schema.py

@@ -386,7 +386,7 @@ def main(schema_directory, output_directory, genes_list, protein_table,
         else:
             # Search for annotations through the SPARQL endpoint
             print('\nQuerying UniProt\'s SPARQL endpoint...')
-            config_file = fo.join_paths(schema_directory, ['.schema_config'])
+            config_file = fo.join_paths(schema_directory, [ct.SCHEMA_CONFIG_BASENAME])
             if os.path.isfile(config_file) is True:
                 config = fo.pickle_loader(config_file)
                 translation_table = config.get('translation_table', [11])[0]