diff data_manager/salmon_index_builder.py @ 0:7d4fd734b078 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/salmon_index_builder.py	Wed Jul 24 07:17:00 2019 -0400
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+# Based heavily on the kallisto data manager wrapper script by iuc
+from __future__ import print_function
+
+import argparse
+import json
+import os
+import subprocess
+import sys
+
+DEFAULT_DATA_TABLE_NAME = "salmon_indexes_versioned"
+
+
+def get_id_name(params, dbkey, fasta_description=None):
+    # TODO: ensure sequence_id is unique and does not already appear in location file
+    sequence_id = params['param_dict']['sequence_id']
+    if not sequence_id:
+        sequence_id = dbkey
+
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = fasta_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return sequence_id, sequence_name
+
+
+def build_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name):
+    data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
+    target_directory = params['output_data' ][0]['extra_files_path']
+    if not os.path.exists(target_directory):
+        os.mkdir(target_directory)
+    args = ['salmon', 'index']
+    if options.kmer_size != '':
+        args.append('-k')
+        args.append(options.kmer_size)
+    args.extend(['-t', options.fasta_filename, '-i', target_directory])
+    return_code = subprocess.call(args=args, shell=False)
+    if return_code:
+        print("Error building index.", file=sys.stderr)
+        sys.exit(return_code)
+    data_table_entry = dict(value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id, version=options.index_version)
+    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+
+
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
+    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
+    return data_manager_dict
+
+
+def main():
+    # Parse Command Line
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--output', dest='output', action='store', type=str, default=None)
+    parser.add_argument('--fasta_filename', dest='fasta_filename', action='store', type=str, default=None)
+    parser.add_argument('--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None)
+    parser.add_argument('--fasta_description', dest='fasta_description', action='store', type=str, default=None)
+    parser.add_argument('--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes')
+    parser.add_argument('-v', '--index_version', dest='index_version', action='store', type=str, help='Use IndexVersion attribute from header.json')
+    parser.add_argument('-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size')
+    options = parser.parse_args()
+
+    filename = options.output
+
+    with open(filename) as fh:
+        params = json.load(fh)
+    data_manager_dict = {}
+
+    if options.fasta_dbkey in [None, '', '?']:
+        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % options.fasta_dbkey)
+
+    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
+    # build the index
+    build_salmon_index(data_manager_dict, options, params, sequence_id, sequence_name)
+
+    # save info to json file
+    with open(filename, 'w') as out:
+        json.dump(data_manager_dict, out, sort_keys=True)
+
+
+if __name__ == "__main__":
+    main()