Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
changeset 4:30fc567efa38 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2017 17:53:33 -0400 |
| parents | a1756ea43ba1 |
| children | d2edf259833c |
| files | data_manager/data_manager_sam_fasta_index_builder.py data_manager/data_manager_sam_fasta_index_builder.xml tool_dependencies.xml |
| diffstat | 3 files changed, 33 insertions(+), 29 deletions(-) [+] |
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--- a/data_manager/data_manager_sam_fasta_index_builder.py Tue Oct 13 10:19:05 2015 -0400 +++ b/data_manager/data_manager_sam_fasta_index_builder.py Tue Apr 04 17:53:33 2017 -0400 @@ -1,5 +1,5 @@ #!/usr/bin/env python -#Dan Blankenberg +# Dan Blankenberg import json import optparse @@ -12,12 +12,13 @@ DEFAULT_DATA_TABLE_NAME = "fasta_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 - + sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = fasta_description @@ -25,16 +26,17 @@ sequence_name = dbkey return sequence_id, sequence_name + def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): - #TODO: allow multiple FASTA input files + # TODO: allow multiple FASTA input files assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename 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 ) - + args = [ 'samtools', 'faidx' ] args.append( sym_linked_fasta_filename ) - tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" ) + tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-sam_fa_index_builder-stderr") proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) return_code = proc.wait() if return_code: @@ -51,37 +53,40 @@ data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) _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 = 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' ) parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) (options, args) = parser.parse_args() - + filename = args[0] - + params = json.loads( open( filename ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) 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 the index build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) - - #save info to json file + + # save info to json file open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) - -if __name__ == "__main__": main() + + +if __name__ == "__main__": + main()
--- a/data_manager/data_manager_sam_fasta_index_builder.xml Tue Oct 13 10:19:05 2015 -0400 +++ b/data_manager/data_manager_sam_fasta_index_builder.xml Tue Apr 04 17:53:33 2017 -0400 @@ -3,23 +3,28 @@ <requirements> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <command interpreter="python">data_manager_sam_fasta_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "fasta_indexes"</command> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/data_manager_sam_fasta_index_builder.py' + '${out_file}' + --fasta_filename '${all_fasta_source.fields.path}' + --fasta_dbkey '${all_fasta_source.fields.dbkey}' + --fasta_description '${all_fasta_source.fields.name}' + --data_table_name fasta_indexes + ]]></command> <inputs> <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta"/> </param> - <param type="text" name="sequence_name" value="" label="Name of sequence" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <param name="sequence_name" type="text" value="" label="Name of sequence" /> + <param name="sequence_id" type="text" value="" label="ID for sequence" /> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> <help> - .. class:: infomark -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - +**Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>
--- a/tool_dependencies.xml Tue Oct 13 10:19:05 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>