| Previous changeset 0:6843a0db2da0 (2017-08-05) Next changeset 2:4c7ebbad42cf (2023-04-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" |
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modified:
data_manager/kallisto_index_builder.py |
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| diff -r 6843a0db2da0 -r 18e2dd472525 data_manager/kallisto_index_builder.py --- a/data_manager/kallisto_index_builder.py Sat Aug 05 04:02:01 2017 -0400 +++ b/data_manager/kallisto_index_builder.py Sun Nov 22 12:50:23 2020 +0000 |
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| @@ -3,15 +3,15 @@ from __future__ import print_function import argparse +import json import os import subprocess import sys -from json import dumps, loads DEFAULT_DATA_TABLE_NAME = "kallisto_indexes" -def get_id_name( params, dbkey, fasta_description=None): +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: @@ -25,57 +25,59 @@ return sequence_id, sequence_name -def build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name ): +def build_kallisto_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 = [ 'kallisto', 'index' ] - args.extend( [ sym_linked_fasta_filename, '-i', sequence_id ] ) - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) + 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 = ['kallisto', 'index'] + args.extend([sym_linked_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 ) + 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 ) +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='kallisto_indexes' ) + 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='kallisto_indexes') options = parser.parse_args() filename = options.output - params = loads( open( filename ).read() ) + 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 ) ) + 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 ) + sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description) # build the index - build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name ) + build_kallisto_index(data_manager_dict, options, params, sequence_id, sequence_name) # save info to json file - open( filename, 'w' ).write( dumps( data_manager_dict ) ) + with open(filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__": |