Mercurial > repos > iuc > data_manager_hisat2_index_builder
view data_manager/hisat2_index_builder.py @ 1:b13b84cb11b5 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit feb20045fb10de6cce2517784f52672322d4d9f8-dirty
author | iuc |
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date | Sat, 10 Oct 2015 16:01:18 -0400 |
parents | d3eb4d51b285 |
children | 98a60a4cfb9a |
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#!/usr/bin/env python # Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg import shlex import sys import os import argparse import subprocess from json import loads, dumps DEFAULT_DATA_TABLE_NAME = "hisat2_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_hisat_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 ) fasta_base_name = os.path.split( options.fasta_filename )[-1] sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) os.symlink( options.fasta_filename, sym_linked_fasta_filename ) args = [ 'hisat2-build' ] args.extend( shlex.split( options.indexer_options ) ) args.extend( [ sym_linked_fasta_filename, sequence_id ] ) proc = subprocess.Popen( args=args, 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=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) _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='hisat2_indexes' ) parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default=None ) options = parser.parse_args() filename = options.output params = loads( open( filename ).read() ) data_manager_dict = {} if options.fasta_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=options.fasta_dbkey, fasta_description=options.fasta_description ) # build the index build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ) # save info to json file open( filename, 'wb' ).write( dumps( data_manager_dict ) ) if __name__ == "__main__": main()