Simplified database download

Now UPIMAPI checks if file exists, if so, it will move forward.
No need for --skip-db-check parameter

upimapi.py

@@ -28,7 +28,7 @@
 from functools import partial
 import re
 
-__version__ = '1.13.0'
+__version__ = '1.13.1'
 
 
 def load_api_info():
@@ -124,7 +124,7 @@ def get_arguments():
         help="If true, UPIMAPI will not check if IDs are valid before mapping [false]")
     parser.add_argument(
         "--skip-db-check", action="store_true", default=False,
-        help="So UPIMAPI doesn't check for (FASTA) database existence [false]")
+        help="DEPRECATED: This parameter does nothing now, and will be removed in future versions.")
     parser.add_argument(
         "--mirror", choices=['expasy', 'uniprot', 'ebi'], default='expasy',
         help="From where to download UniProt database [expasy]")
@@ -800,7 +800,7 @@ def download_uniprot(output_folder, mirror='expasy'):
         os.remove(file)
 
 
-def build_reference_database(database, output_folder, taxids=None, max_tries=3, mirror='expasy'):
+def download_fasta_database(database, output_folder, taxids=None, max_tries=3, mirror='expasy'):
     if database == 'uniprot':
         download_uniprot(output_folder, mirror=mirror)
     elif database == 'swissprot':
@@ -814,12 +814,10 @@ def build_reference_database(database, output_folder, taxids=None, max_tries=3,
                 f.write(get_proteome_for_taxid(taxid, max_tries=max_tries))
 
 
-def must_build_database(database, resources_folder):
-    db2suffix = {'uniprot': 'uniprot.fasta', 'swissprot': 'uniprot_sprot.fasta', 'taxids': 'taxids_database.fasta'}
+def must_download_database(database, db2suffix):
     if database in db2suffix.keys():
-        if os.path.isfile(f'{resources_folder}/{db2suffix[database]}'):
-            return str2bool(input(f'{resources_folder}/{db2suffix[database]} exists. Overwrite? [Y/N] '))
-    return True
+        return not os.path.isfile(db2suffix[database])
+    return False        # custom database
 
 
 def get_tabular_taxonomy(output):
@@ -1342,24 +1340,27 @@ def upimapi():
 
     # Annotation with DIAMOND
     if not args.no_annotation:
-        db2file = {'uniprot': f'{args.resources_directory}/uniprot.fasta',
-                   'swissprot': f'{args.resources_directory}/uniprot_sprot.fasta',
-                   'taxids': f'{args.resources_directory}/taxids_database.fasta'}
+        db2file = {db: f'{args.resources_directory}/{filename}' for db, filename in [
+            ('uniprot', 'uniprot.fasta'), ('swissprot', 'uniprot_sprot.fasta'), ('taxids', 'taxids_database.fasta')]}
         if args.database in db2file.keys():
             database = db2file[args.database]
         else:
-            database = args.database
-
-        if not args.skip_db_check:
-            if must_build_database(args.database, args.resources_directory):
-                build_reference_database(
-                    args.database, args.resources_directory, taxids=args.taxids, max_tries=args.max_tries,
-                    mirror=args.mirror)
-        if not database.endswith(".dmnd"):
+            database = args.database        # custom database, must have UniProt IDs as sequence names
+
+        if not database.endswith(".dmnd"):                  # database is FASTA or one of "uniprot", "swissprot" or "taxids", or not valid
             diamond_formatted = f"{'.'.join(database.split('.')[:-1])}.dmnd"
-            if not os.path.isfile(diamond_formatted):
+            if not os.path.isfile(diamond_formatted):               # DMND version of database not available
+                if must_download_database(args.database, db2file):  # check if expected FASTA file exists
+                    print(f'{args.database} database not found at {args.resources_directory}. '
+                          f'Downloading in FASTA version.')
+                    download_fasta_database(
+                        args.database, args.resources_directory, taxids=args.taxids, max_tries=args.max_tries,
+                        mirror=args.mirror)
+                print(f'DMND formatted version of database not found at: {diamond_formatted}')
                 make_diamond_database(database, diamond_formatted)
             database = diamond_formatted
+        if not os.path.isfile(database):
+            sys.exit(f'Database [{database}] not found! Exiting...')  # only happens for DMND or custom databases
         (b, c) = block_size_and_index_chunks(
             argsb=args.block_size, argsc=args.index_chunks, memory=args.max_memory)
         run_diamond(