Add hmmer transformation step

dbman/helper.py

@@ -15,14 +15,20 @@ def download(url):
   print("") # wget does not add a newline to its download bar
   return filename
 
-def extract(filename):
+def extract(filename, target_dir=None):
   logging.info("Extracting " + filename)
   if '.tar.' in filename:
     with tarfile.open(filename, 'r') as tar:
       tar.extractall()
+      return '.'
   elif filename.endswith(".gz"):
-    with gzip.open(filename, 'rb') as gin, open(re.sub("\.gz$", "", filename), 'wb') as bout:
+    target_file = re.sub("\.gz$", "", filename)
+    if target_dir:
+      target_file = os.path.join(target_dir, os.path.basename(target_file))
+
+    with gzip.open(filename, 'rb') as gin, open(target_file, 'wb') as bout:
       shutil.copyfileobj(gin, bout)
+      return target_file
   else:
     raise Exception("Compression not supported")
 

dbman/main.py

@@ -164,7 +164,9 @@ def run_in_tempdir(func=None, success=None, fail=None):
 
 def _recipes(args):
    recipes = {
-     'pfam': {'download': {'script': _pkgres('recipes/download_pfam.py')}},
+     'pfam': {'download': {'script': _pkgres('recipes/download_pfam.py')},
+              'hmmer': {'script': _pkgres('recipes/create_hmmer_dbs.py')},
+              },
      'card': {'download': {'script': _pkgres('recipes/download_card.py')},
               'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
               'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')},

dbman/recipes/create_hmmer_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')
+
+hmm_profile_parts = [p for p in metadata['parts'] if 'hmm' in p['tags'] and 'profile' in p['tags']]
+new_parts = []
+for part in hmm_profile_parts:
+  # temporalily uncompress for hmmpress, as it can't handle gzip files
+  files = []
+  if 'gzip' in part['tags']:
+    for file in part['files']:
+      fn = h.extract(file, './')
+      files.append(fn)
+  else:
+    files = part['files']
+
+  for file in files:
+    name = Path(file).stem
+    command = 'hmmpress {}'.format(file)
+    cp = subprocess.run(command, shell=True)
+    if (cp.returncode != 0):
+      sys.exit(cp)
+
+    # remove unzipped files
+    if 'gzip' in part['tags']:
+      for file in files:
+        os.unlink(file)
+
+    files = [f.name for f in os.scandir('.') if f.name.startswith(name + '.') and not f.name.endswith('.')]
+
+    tags = ['hmm_profile_db']
+    tags.extend(part['tags'])
+    tags.remove('gzip')
+    tags.remove('compressed')
+
+    new_parts.append({'files': files, 'tags': tags})
+    
+h.create_metadata(metadata['name'], 'hmmer', metadata['description'], metadata['version'], other={'parts': new_parts})