diff data_manager/bracken_build_database.py @ 0:911bb6c95bf8 draft default tip

"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit d0b060e7d9cc9fd89926dbc07fc93c8a1471b3fe-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bracken_build_database.py	Thu Oct 24 17:44:45 2019 -0400
@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import errno
+import json
+import os
+import subprocess
+import uuid
+
+
+DATA_TABLE_NAME = "bracken_databases"
+
+
+def bracken_build_database(target_directory, bracken_build_args, database_name, data_table_name=DATA_TABLE_NAME):
+
+    database_value = str(uuid.uuid4())
+
+    database_name = database_name
+
+    database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib')
+
+    bracken_build_args_list = [
+        '-t', bracken_build_args['threads'],
+        '-k', bracken_build_args['kmer_len'],
+        '-l', bracken_build_args['read_len'],
+        '-d', bracken_build_args['kraken_database'],
+    ]
+
+    subprocess.check_call(['bracken-build'] + bracken_build_args_list)
+
+    data_table_entry = {
+        "data_tables": {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('data_manager_json')
+    parser.add_argument('--threads', dest='threads', default=1, help='threads')
+    parser.add_argument('--kmer-len', dest='kmer_len', help='K-mer length')
+    parser.add_argument('--read-len', dest='read_len', help='Read length')
+    parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database')
+    parser.add_argument('--database-name', dest='database_name', help='Database Name')
+    args = parser.parse_args()
+
+    data_manager_input = json.loads(open(args.data_manager_json).read())
+
+    target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+    bracken_build_args = {
+        'threads': args.threads,
+        'kmer_len': args.kmer_len,
+        'read_len': args.read_len,
+        'kraken_database': args.kraken_database,
+    }
+
+    try:
+        os.mkdir(target_directory)
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+            pass
+        else:
+            raise
+
+    data_manager_output = {}
+
+    data_manager_output = bracken_build_database(
+        target_directory,
+        bracken_build_args,
+        args.database_name,
+    )
+
+    with open(args.data_manager_json, 'w') as out:
+        out.write(json.dumps(data_manager_output, sort_keys=True))
+
+
+if __name__ == "__main__":
+    main()