changeset 9:47432d88b0a0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 9fa01fe96452d50646e066066b1e556ba4a75ced"
author iuc
date Mon, 06 Apr 2020 23:13:03 +0000
parents 62f1a6310409
children e816eef8a48f
files data_manager/bowtie2_index_builder.py
diffstat 1 files changed, 26 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/bowtie2_index_builder.py	Sun Dec 22 15:34:40 2019 +0000
+++ b/data_manager/bowtie2_index_builder.py	Mon Apr 06 23:13:03 2020 +0000
@@ -11,7 +11,7 @@
 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_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:
@@ -25,60 +25,60 @@
     return sequence_id, sequence_name
 
 
-def build_bowtie2_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+def build_bowtie2_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
     # 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 )
-    args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ]
+    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 = ['bowtie2-build', sym_linked_fasta_filename, sequence_id]
     threads = os.environ.get('GALAXY_SLOTS')
     if threads:
         args.extend(['--threads', threads])
-    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+    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=dbkey, name=sequence_name, path=sequence_id )
+        sys.exit(return_code)
+    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
     for data_table_name in data_table_names:
-        _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+        _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():
     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='append', type="string", default=None, help='data_table_name' )
+    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='append', type="string", default=None, help='data_table_name')
     (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 )
+    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 ) )
+    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 )
+    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
 
     # build the index
-    build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES )
+    build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
 
     # save info to json file
     with open(filename, 'w') as json_out:
-        json_out.write( dumps( data_manager_dict, sort_keys=True ) )
+        json_out.write(dumps(data_manager_dict, sort_keys=True))
 
 
 if __name__ == "__main__":