| Previous changeset 1:df883cc67fbd (2017-01-19) Next changeset 3:5c77d4091880 (2019-11-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f |
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modified:
data_manager/twobit_builder.py data_manager/twobit_builder.xml |
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| diff -r df883cc67fbd -r 9946bc39c834 data_manager/twobit_builder.py --- a/data_manager/twobit_builder.py Thu Jan 19 11:45:43 2017 -0500 +++ b/data_manager/twobit_builder.py Tue Apr 04 18:16:29 2017 -0400 |
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| @@ -1,19 +1,23 @@ #!/usr/bin/env python -#Dan Blankenberg +# Dan Blankenberg +from __future__ import print_function -import sys, os, tempfile, optparse, uuid, subprocess +import optparse +import os +import subprocess +import sys +import tempfile +from json import dumps, loads -from json import loads, dumps +CHUNK_SIZE = 2**20 # 1mb -CHUNK_SIZE = 2**20 #1mb - 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 #uuid.uuid4() generate and use an uuid - + sequence_id = dbkey # uuid.uuid4() generate and use an uuid + sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = fasta_description @@ -21,18 +25,19 @@ sequence_name = dbkey return sequence_id, sequence_name + def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ): twobit_base_name = "%s.2bit" % ( sequence_id ) twobit_filename = os.path.join( target_directory, twobit_base_name ) - + args = [ 'faToTwoBit', fasta_filename, twobit_filename ] - tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-twobit-builder-stderr" ) + tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-twobit-builder-stderr" ) proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) return_code = proc.wait() if return_code: tmp_stderr.flush() tmp_stderr.seek(0) - print >> sys.stderr, "Error building index:" + print("Error building index:", file=sys.stderr) while True: chunk = tmp_stderr.read( CHUNK_SIZE ) if not chunk: @@ -40,53 +45,55 @@ sys.stderr.write( chunk ) sys.exit( return_code ) tmp_stderr.close() - #lastz_seqs + # lastz_seqs data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name ) _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry ) - #twobit.loc + # twobit.loc data_table_entry = dict( value=sequence_id, path=twobit_base_name ) _add_data_table_entry( data_manager_dict, "twobit", data_table_entry ) - #alignseq + # alignseq data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name ) _add_data_table_entry( data_manager_dict, "alignseq_seq", 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' ) (options, args) = parser.parse_args() - + filename = args[0] - + params = loads( open( filename ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) data_manager_dict = {} - + dbkey = options.fasta_dbkey - + if 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=dbkey, fasta_description=options.fasta_description ) - - #build the index + + # build the index build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ) - - #save info to json file + + # save info to json file open( filename, 'wb' ).write( dumps( data_manager_dict ) ) - -if __name__ == "__main__": main() + +if __name__ == "__main__": + main() |
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| diff -r df883cc67fbd -r 9946bc39c834 data_manager/twobit_builder.xml --- a/data_manager/twobit_builder.xml Thu Jan 19 11:45:43 2017 -0500 +++ b/data_manager/twobit_builder.xml Tue Apr 04 18:16:29 2017 -0400 |
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| @@ -3,14 +3,19 @@ <requirement type="package" version="324">ucsc-fatotwobit</requirement> </requirements> <description>builder</description> - <command interpreter="python">twobit_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}"</command> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/twobit_builder.py' + '${out_file}' + --fasta_filename '${all_fasta_source.fields.path}' + --fasta_dbkey '${all_fasta_source.fields.dbkey}' + --fasta_description '${all_fasta_source.fields.name}' + ]]></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"/> @@ -25,11 +30,9 @@ </tests> <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> |