Add ghostx db creation

dbman/main.py

@@ -141,7 +141,8 @@ def _rename_directory_after_metadata(path):
     logging.debug("Renaming '%s' to '%s'", oldpath, newpath)
     oldpath.rename(newpath)
     metadata['location'] = str(newpath.absolute())
-  return metadata
+    return metadata
+  return None
 
 def run_in_tempdir(func=None, success=None, fail=None):
   dbtmpdir = os.path.join(_databases_dir(), "tmp")
@@ -166,10 +167,12 @@ def _recipes(args):
      'card': {'download': {'script': _pkgres('recipes/download_card.py')},
               'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
               'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')},
+              'ghostx': {'script': _pkgres('recipes/create_ghostx_dbs.py')},
               },
      'swissprot': {'download': {'script': _pkgres('recipes/download_uniprotkb.py'), 'params': ['--database', 'swissprot', '--type', 'fasta']},
                    'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
                    'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')},
+                   'ghostx': {'script': _pkgres('recipes/create_ghostx_dbs.py')},
                   }
    }
    return recipes

dbman/recipes/create_ghostx_dbs.py

+#!/usr/bin/env python
+import dbman.helper as h
+import subprocess
+import sys
+import os
+import json
+from pathlib import Path
+
+metadata = h.load_metadata('./.source_metadata.json')
+
+fasta_parts = [p for p in metadata['parts'] if 'fasta' in p['tags']]
+new_parts = []
+for part in fasta_parts:
+  type = None
+
+  for file in part['files']:
+    name = Path(file).stem
+    command = 'ghostx db -o {} -i {}'.format(name, file)
+    cp = subprocess.run(command, shell=True)
+    if (cp.returncode != 0):
+      sys.exit(cp)
+    files = [f.name for f in os.scandir('.') if f.name.startswith(name) and not f.name.endswith('.fasta')]
+
+    tags = ['ghostx_db']
+    tags.extend(part['tags'])
+    tags.remove('fasta')
+
+    new_parts.append({'files': files, 'tags': tags})
+
+h.create_metadata(metadata['name'], 'ghostx', metadata['description'], metadata['version'], other={'parts': new_parts})