Mercurial > repos > iuc > data_manager_bowtie_index_builder
changeset 1:35c1e3785c90 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
| author | iuc |
|---|---|
| date | Sun, 18 Sep 2016 07:22:06 -0400 |
| parents | 0a0c648498e2 |
| children | 086edfff112b |
| files | data_manager/bowtie_index_builder.py |
| diffstat | 1 files changed, 14 insertions(+), 17 deletions(-) [+] |
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--- a/data_manager/bowtie_index_builder.py Tue Jan 05 12:57:11 2016 -0500 +++ b/data_manager/bowtie_index_builder.py Sun Sep 18 07:22:06 2016 -0400 @@ -1,20 +1,18 @@ #!/usr/bin/env python - +import json +import optparse +import os +import subprocess import sys -import os import tempfile -import optparse -import subprocess - -from galaxy.util.json import from_json_string, to_json_string - CHUNK_SIZE = 2**20 DEFAULT_DATA_TABLE_NAME = "bowtie_indexes" + def get_id_name( params, dbkey, fasta_description=None): - #TODO: ensure sequence_id is unique and does not already appear in location file + # 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 @@ -27,9 +25,8 @@ return sequence_id, sequence_name -def build_bowtie_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space = False ): - #TODO: allow multiple FASTA input files - #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bowtie-index-builder-' ) +def build_bowtie_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space=False ): + # 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 ) @@ -39,7 +36,7 @@ args.append( sym_linked_fasta_filename) args.append( fasta_base_name ) args.append( sym_linked_fasta_filename ) - tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-bowtie-index-builder-stderr" ) + tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-bowtie-index-builder-stderr" ) proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) return_code = proc.wait() if return_code: @@ -65,7 +62,7 @@ def main(): - #Parse Command Line + # Parse Command Line 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' ) @@ -76,7 +73,7 @@ filename = args[0] - params = from_json_string( open( filename ).read() ) + params = json.loads( open( filename ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) data_manager_dict = {} @@ -88,11 +85,11 @@ sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) - #build the index + # build the index build_bowtie_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space ) - #save info to json file - open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) + # save info to json file + open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) if __name__ == "__main__": main()