disable download HMM databases (until ready)

eggnogdb · Apr 15, 2019 · df8069a · df8069a
1 parent d63c728
commit df8069a
Showing 1 changed file with 24 additions and 24 deletions.
diff --git a/download_eggnog_data.py b/download_eggnog_data.py
@@ -55,8 +55,8 @@ def download_og2level():
 
 if __name__ == "__main__":
     parser = ArgumentParser()
-    parser.add_argument('dbs', metavar='dbs', nargs='+', choices=sorted(EGGNOG_DATABASES.keys()+['all', 'none']),
-                        help='list of eggNOG HMM databases to download. Choose "none" if only diamond will be used')
+    # parser.add_argument('dbs', metavar='dbs', nargs='+', choices=sorted(EGGNOG_DATABASES.keys()+['all', 'none']),
+    #                     help='list of eggNOG HMM databases to download. Choose "none" if only diamond will be used')
 
     parser.add_argument('-D', action="store_true", dest='skip_diamond',
                         help='Do not install the diamond database')
@@ -82,12 +82,12 @@ def download_og2level():
     if args.data_dir:
         set_data_path(args.data_dir)
 
-    if args.force or not pexists(pjoin(get_data_path(), 'og2level.tsv.gz')):
-        print colorify('Downloading "og2level.tsv.gz" at %s' %get_data_path(), 'green')
-        download_og2level()
+    # if args.force or not pexists(pjoin(get_data_path(), 'og2level.tsv.gz')):
+    #     print colorify('Downloading "og2level.tsv.gz" at %s' %get_data_path(), 'green')
+    #     download_og2level()
 
-    if 'all' in args.dbs:
-        args.dbs = EGGNOG_DATABASES
+    # if 'all' in args.dbs:
+    #     args.dbs = EGGNOG_DATABASES
 
     if args.force or not pexists(pjoin(get_data_path(), 'eggnog.db')):
         if args.allyes or ask("Download main annotation database?") == 'y':
@@ -100,16 +100,16 @@ def download_og2level():
         if not args.quiet:
             print colorify('Skipping eggnog.db database (already present). Use -f to force download', 'lblue')
 
-    if args.force or not pexists(pjoin(get_data_path(), 'OG_fasta')):
-        if args.allyes or ask("Download OG fasta files for annotation refinement (~20GB after decompression)?") == 'y':
-            print colorify('Downloading fasta files " at %s/OG_fasta...' %get_data_path(), 'green')
-            download_groups()
-        else:
-            print 'Skipping'
+    # if args.force or not pexists(pjoin(get_data_path(), 'OG_fasta')):
+    #     if args.allyes or ask("Download OG fasta files for annotation refinement (~20GB after decompression)?") == 'y':
+    #         print colorify('Downloading fasta files " at %s/OG_fasta...' %get_data_path(), 'green')
+    #         download_groups()
+    #     else:
+    #         print 'Skipping'
 
-    else:
-        if not args.quiet:
-            print colorify('Skipping OG_fasta/ database (already present). Use -f to force download', 'lblue')
+    # else:
+    #     if not args.quiet:
+    #         print colorify('Skipping OG_fasta/ database (already present). Use -f to force download', 'lblue')
 
     if not args.skip_diamond and (args.force or not pexists(pjoin(get_data_path(), 'eggnog_proteins.dmnd'))):
         if args.allyes or ask("Download diamond database (~4GB after decompression)?") == 'y':
@@ -121,11 +121,11 @@ def download_og2level():
         if not args.quiet:
             print colorify('Skipping diamond database (or already present). Use -f to force download', 'lblue')
 
-    if set(args.dbs) != set(['none']):
-        if args.allyes or ask("Download %d HMM database(s): %s?"%(len(args.dbs), ','.join(args.dbs))) == 'y':
-            for db in args.dbs:
-                if args.force or not get_db_present(db):
-                    print colorify('Downloading %s HMM database " at %s/%s\_hmm ...' %(db, get_hmmdb_path(), db), 'green')
-                    download_hmm_database(db)
-        else:
-            print 'Skipping'
+    # if set(args.dbs) != set(['none']):
+    #     if args.allyes or ask("Download %d HMM database(s): %s?"%(len(args.dbs), ','.join(args.dbs))) == 'y':
+    #         for db in args.dbs:
+    #             if args.force or not get_db_present(db):
+    #                 print colorify('Downloading %s HMM database " at %s/%s\_hmm ...' %(db, get_hmmdb_path(), db), 'green')
+    #                 download_hmm_database(db)
+    #     else:
+    #         print 'Skipping'