--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bowtie2_index_builder.py	Thu Apr 02 13:16:53 2020 +0000
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+# Dan Blankenberg
+from __future__ import print_function
+
+import optparse
+import os
+import subprocess
+import sys
+from json import dumps, loads
+
+DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"]
+
+
+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_bowtie2_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+    # TODO: allow multiple FASTA input files
+    fasta_base_name = os.path.split(fasta_filename)[-1]
+    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
+    os.symlink(fasta_filename, sym_linked_fasta_filename)
+    args = ['bowtie2-build', sym_linked_fasta_filename, sequence_id]
+    threads = os.environ.get('GALAXY_SLOTS')
+    if threads:
+        args.extend(['--threads', threads])
+    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+    return_code = proc.wait()
+    if return_code:
+        print("Error building index.", file=sys.stderr)
+        sys.exit(return_code)
+    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
+    for data_table_name in data_table_names:
+        _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():
+    parser = optparse.OptionParser()
+    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
+    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
+    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
+    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name')
+    (options, args) = parser.parse_args()
+
+    filename = args[0]
+
+    params = loads(open(filename).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    data_manager_dict = {}
+
+    dbkey = options.fasta_dbkey
+
+    if dbkey in [None, '', '?']:
+        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
+
+    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
+
+    # build the index
+    build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
+
+    # save info to json file
+    with open(filename, 'w') as json_out:
+        json_out.write(dumps(data_manager_dict, sort_keys=True))
+
+
+if __name__ == "__main__":
+    main()