Commit 57002a0c authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Add ghostx db creation

parent be780604
...@@ -141,7 +141,8 @@ def _rename_directory_after_metadata(path): ...@@ -141,7 +141,8 @@ def _rename_directory_after_metadata(path):
logging.debug("Renaming '%s' to '%s'", oldpath, newpath) logging.debug("Renaming '%s' to '%s'", oldpath, newpath)
oldpath.rename(newpath) oldpath.rename(newpath)
metadata['location'] = str(newpath.absolute()) metadata['location'] = str(newpath.absolute())
return metadata return metadata
return None
def run_in_tempdir(func=None, success=None, fail=None): def run_in_tempdir(func=None, success=None, fail=None):
dbtmpdir = os.path.join(_databases_dir(), "tmp") dbtmpdir = os.path.join(_databases_dir(), "tmp")
...@@ -166,10 +167,12 @@ def _recipes(args): ...@@ -166,10 +167,12 @@ def _recipes(args):
'card': {'download': {'script': _pkgres('recipes/download_card.py')}, 'card': {'download': {'script': _pkgres('recipes/download_card.py')},
'blast': {'script': _pkgres('recipes/create_blast_dbs.py')}, 'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
'diamond': {'script': _pkgres('recipes/create_diamond_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']}, 'swissprot': {'download': {'script': _pkgres('recipes/download_uniprotkb.py'), 'params': ['--database', 'swissprot', '--type', 'fasta']},
'blast': {'script': _pkgres('recipes/create_blast_dbs.py')}, 'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')}, 'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')},
'ghostx': {'script': _pkgres('recipes/create_ghostx_dbs.py')},
} }
} }
return recipes return recipes
......
#!/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})
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