Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
diff data_manager/salmon_index_builder.py @ 1:c5dea2080109 draft
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author | ieguinoa |
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date | Tue, 14 Aug 2018 11:19:49 -0400 |
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children | f7d9182bdcab |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/salmon_index_builder.py Tue Aug 14 11:19:49 2018 -0400 @@ -0,0 +1,82 @@ +#!/usr/bin/env python +# Based heavily on the kallisto data manager wrapper script by iuc +from __future__ import print_function + +import argparse +import os +import subprocess +import sys +from json import dumps, loads + +DEFAULT_DATA_TABLE_NAME = "salmon_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_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 ) + if options.kmer_size != '': + args.append('-k') + args.append(options.kmer_size) + args.extend( [ '-t' , options.fasta_filename, '-i', sequence_id ] ) + 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=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='salmon_indexes' ) + parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' ) + 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.' % ( 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 + open( filename, 'w' ).write( dumps( data_manager_dict ) ) + + +if __name__ == "__main__": + main()