Add resfinder download

dbman/main.py

@@ -164,24 +164,34 @@ def run_in_tempdir(func=None, success=None, fail=None):
 
 def _recipes(args):
    recipes = {
-     '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')},
-              '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')},
-                  },
-     'trembl': {'download': {'script': _pkgres('recipes/download_uniprotkb.py'), 'params': ['--database', 'trembl', '--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')},
-                  }
+     'resfinder': {
+       'download': {'script': _pkgres('recipes/download_resfinder.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')},
+     },
+     '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')},
+       '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')},
+     },
+     'trembl': {
+       'download': {'script': _pkgres('recipes/download_uniprotkb.py'), 'params': ['--database', 'trembl', '--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/download_resfinder.py

+#!/usr/bin/env python3
+import dbman.helper as h
+import json
+import os
+import gzip
+import subprocess
+import shutil
+from pathlib import Path
+
+import logging
+logging.basicConfig(level=logging.INFO)
+
+dbname = "resfinder"
+dbdescription = "The ResFinder database is a curated database of acquired resistance genes."
+url = "https://git@bitbucket.org/genomicepidemiology/resfinder_db.git"
+
+# clone git repo
+command = "git clone {}".format(url)
+cp = subprocess.run(command, shell=True)
+if cp.returncode != 0:
+  sys.exit(cp.returncode)
+
+parts = []
+fastas = Path('resfinder_db').rglob("*.fsa")
+for file in fastas:
+  target = file.resolve().parent.parent.joinpath(file.name)
+  file.rename(target)
+  parts.append({'files': [target.name], 'tags': ['fasta', 'nucleotide']})
+txts = Path('resfinder_db').rglob("*.txt")
+for file in txts:
+  target = file.resolve().parent.parent.joinpath(file.name)
+  file.rename(target)
+  parts.append({'files': [target.name], 'tags': ['text', 'annotation']})
+
+shutil.rmtree('resfinder_db')
+
+# write metadata file
+h.create_metadata(dbname, "download", dbdescription, other={'parts': parts})