diff data_manager/bwa_index_builder.py @ 0:ae10d0ddbbb1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bwa_index_builder.py	Fri Nov 06 14:15:00 2015 -0500
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import optparse
+import subprocess
+
+from json import loads, dumps
+
+
+CHUNK_SIZE = 2**20
+ONE_GB = 2**30
+
+DEFAULT_DATA_TABLE_NAME = "bwa_indexes"
+
+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:
+        sequence_id = dbkey
+    
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = fasta_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return sequence_id, sequence_name
+
+def build_bwa_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-bwa-index-builder-' )
+    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 )
+    if params['param_dict']['index_algorithm'] == 'automatic':
+        if os.stat( fasta_filename ).st_size <= ONE_GB: #use 1 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary
+            index_algorithm = 'is'
+        else:
+            index_algorithm = 'bwtsw'
+    else:
+        index_algorithm = params['param_dict']['index_algorithm']
+    
+    args = [ 'bwa', 'index', '-a', index_algorithm ]
+    if color_space:
+        args.append( '-c' )
+    args.append( sym_linked_fasta_filename )
+    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+    return_code = proc.wait()
+    if return_code:
+        print >> sys.stderr, "Error building index."
+        sys.exit( return_code )
+    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' )
+    parser.add_option( '-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space' )
+    (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_bwa_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( dumps( data_manager_dict ) )
+        
+if __name__ == "__main__": main()