New parameter - output-rpsbproc-columns

Now by default reCOGnizer doesn't include the three columns that are always almost empty from analysis with rpsbproc
Fix on reporting download files
It was only reporting it when it removed files

recognizer.py

@@ -8,7 +8,6 @@
 """
 
 import shutil
-import warnings
 from argparse import ArgumentParser, ArgumentTypeError
 from glob import glob
 import os
@@ -69,6 +68,9 @@ def get_arguments():
     parser.add_argument(
         "--no-blast-info", action="store_true", default=False,
         help="Information from the alignment will be stored in their own columns.")
+    parser.add_argument(
+        "--output-rpsbproc-cols", action="store_true", default=False,
+        help="Output columns obtained with RPSBPROC - 'Superfamilies', 'Sites' and 'Motifs'.")
     parser.add_argument(
         "-sd", "--skip-downloaded", default=None,
         help="This parameter is deprecated. Please do not use it [None]")
@@ -134,7 +136,7 @@ def get_arguments():
 
     if args.file:
         for directory in [f'{args.output}/{folder}' for folder in ['asn', 'blast', 'rpsbproc', 'tmp']] + [
-            f'{args.resources_directory}/dbs']:
+                f'{args.resources_directory}/dbs']:
             if not os.path.isdir(directory):
                 Path(directory).mkdir(parents=True, exist_ok=True)
                 print(f'Created {directory}')
@@ -246,8 +248,7 @@ def download_resources(directory, quiet=False, test_run=False):
         if os.path.isfile(f"{directory}/{filename}"):
             print(f"Removing {directory}/{filename}")
             os.remove(f"{directory}/{filename}")
-            if quiet:
-                print(f'Downloading {location}')  # quiet replaces all wget output with this simple message
+        print(f'Downloading {location}')
         run_command(f'wget {location} -P {directory}{" -q" if quiet else ""}')
         if filename.endswith('.gz') and not filename.endswith('.tar.gz'):
             if os.path.isfile(f"{directory}/{filename}"[:-3]):  # filename without .gz
@@ -950,18 +951,21 @@ def complete_report(report, db, resources_directory, output, hmm_pgap, fun):
     return report[cols].rename(columns={'product_name': 'Protein description', 'ec_number': 'EC number'})
 
 
-def organize_results(file, output, resources_directory, databases, hmm_pgap, cddid, fun, no_output_sequences=False):
+def organize_results(
+        file, output, resources_directory, databases, hmm_pgap, cddid, fun, no_output_sequences=False,
+        include_rpsbproc_cols=False):
     timed_message("Organizing annotation results")
     i = 1
     xlsx_report = pd.ExcelWriter(f'{output}/reCOGnizer_results.xlsx', engine='xlsxwriter')
-    all_reports = pd.DataFrame(columns=['qseqid',
-                                        'DB ID'])  # intialize with these columns so if it has no rows, at least it has the columns to groupby
+    all_reports = pd.DataFrame(columns=['qseqid', 'DB ID'])     # intialize with these columns so if it has no rows, at least it has the columns to groupby
     for db in databases:
         run_pipe_command(f'cat {output}/blast/{db}_*_aligned.blast', file=f'{output}/blast/{db}_aligned.blast')
         print(f'[{i}/{len(databases)}] Handling {db} annotation')
         blast_res = parse_blast(f'{output}/blast/{db}_aligned.blast')
         if db != 'KOG':  # rpsbproc doesn't work with KOG
             rpsbproc_res = pd.read_csv(f'{output}/rpsbproc/{db}_report.tsv', sep='\t', index_col=0)
+            if not include_rpsbproc_cols:
+                rpsbproc_res.drop(columns=['Superfamilies', 'Sites', 'Motifs'], inplace=True)
             report = pd.merge(rpsbproc_res, blast_res, on=['qseqid', 'sseqid'], how='left')
         else:
             report = blast_res
@@ -990,12 +994,12 @@ def main():
     cddid, hmm_pgap, fun, taxonomy_df, members_df = load_relational_tables(
         args.resources_directory, tax_file=args.tax_file)
 
-    if not args.keep_spaces:
-        args.file = replace_spaces_with_underscores(args.file,
-                                                    f'{args.output}/tmp')  # if alters input file, internally alters args.file
+    if not args.keep_spaces:       # if alters input file, internally alters args.file
+        args.file = replace_spaces_with_underscores(args.file, f'{args.output}/tmp')
 
-    split_fasta_by_threads(args.file, f'{args.output}/tmp/tmp',
-                           args.threads)  # this splitting is always necessary, even with taxonomy inputted, since some databases don't have taxonomy-based annotation
+    # this splitting is always necessary, even with taxonomy inputted, since some databases don't have taxonomy-based
+    # annotation. And it keeps things simpler.
+    split_fasta_by_threads(args.file, f'{args.output}/tmp/tmp', args.threads)
     if args.custom_databases:
         custom_database_workflow(
             args.output, args.databases, threads=args.threads, max_target_seqs=args.max_target_seqs, evalue=args.evalue)
@@ -1009,6 +1013,8 @@ def main():
                 if os.path.isfile(f'{args.output}/tmp/{taxid}.fasta'):
                     split_fasta_by_threads(
                         f'{args.output}/tmp/{taxid}.fasta', f'{args.output}/tmp/tmp_{taxid}', args.threads)
+        else:
+            tax_file = lineages = all_taxids = None
         databases_prefixes = {
             'CDD': 'cd', 'Pfam': 'pfam', 'NCBIfam': 'NF', 'Protein_Clusters': 'PRK', 'Smart': 'smart',
             'TIGRFAM': 'TIGR', 'COG': 'COG', 'KOG': 'KOG'}
@@ -1029,7 +1035,7 @@ def main():
                     max_target_seqs=args.max_target_seqs, evalue=args.evalue)
         organize_results(
             args.file, args.output, args.resources_directory, args.databases, hmm_pgap, cddid, fun,
-            no_output_sequences=args.no_output_sequences)
+            no_output_sequences=args.no_output_sequences, include_rpsbproc_cols=args.output_rpsbproc_cols)
         if not args.keep_intermediates:
             for directory in [f'{args.output}/{folder}' for folder in ['asn', 'blast', 'rpsbproc', 'tmp']]:
                 shutil.rmtree(directory)