Mercurial > repos > iuc > data_manager_bwameth_index_builder
diff data_manager/bwameth_index_builder.py @ 0:a7fb84abef45 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
author | iuc |
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date | Tue, 22 Nov 2016 17:12:00 -0500 |
parents | |
children | e7ca32457e36 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/bwameth_index_builder.py Tue Nov 22 17:12:00 2016 -0500 @@ -0,0 +1,64 @@ +#!/usr/bin/env python +# Based heavily on the HISAT2 data manager wrapper + +import argparse +import os +import subprocess +import sys +from json import dumps, loads + +DEFAULT_DATA_TABLE_NAME = "bwameth_indexes" + + +def build_bwameth_index(data_manager_dict, params, args): + data_table_name = args.data_table_name + target_directory = params[ 'output_data' ][0]['extra_files_path'] + if not os.path.exists( target_directory ): + os.mkdir( target_directory ) + fasta_base_name = os.path.basename(args.fasta_filename) + sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) + os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename) + cmd = ['bwameth.py', 'index', sym_linked_fasta_filename] + proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory) + return_code = proc.wait() + if return_code: + print >> sys.stderr, "Error building index." + sys.exit( return_code ) + data_table_entry = dict(value=args.dbKey, dbkey=args.dbkey, name=args.name, path=args.dbKey) + _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', default=None ) + parser.add_argument( '--fasta_filename', default=None ) + parser.add_argument( '--dbkey', default=None ) + parser.add_argument( '--name', default=None ) + parser.add_argument( '--description', default=None ) + parser.add_argument( '--data_table_name', default=DEFAULT_DATA_TABLE_NAME ) + args = parser.parse_args() + + filename = args.output + params = loads(open(filename).read()) + data_manager_dict = {} + + if args.dbkey in [ None, '', '?' ]: + raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey)) + + # build the index + build_bwameth_index(data_manager_dict, params, args) + + # save info to json file + open(filename, 'wb').write(dumps(data_manager_dict)) + + +if __name__ == "__main__": + main()