# HG changeset patch
# User iuc
# Date 1491343624 14400
# Node ID 46066df8813dfa30d1dd76e817ffbc3fd4a4b179
# Parent 414a92a973fa6474726974900375fb4539091492
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
diff -r 414a92a973fa -r 46066df8813d data_manager/bwa_mem_index_builder.py
--- a/data_manager/bwa_mem_index_builder.py Thu Jan 19 11:48:36 2017 -0500
+++ b/data_manager/bwa_mem_index_builder.py Tue Apr 04 18:07:04 2017 -0400
@@ -1,26 +1,24 @@
#!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
+from __future__ import print_function
-import sys
+import optparse
import os
-import tempfile
-import optparse
import subprocess
+import sys
+from json import dumps, loads
-from json import loads, dumps
+CHUNK_SIZE = 2**20
+TWO_GB = 2**30 * 2
+DEFAULT_DATA_TABLE_NAME = "bwa_mem_indexes"
-CHUNK_SIZE = 2**20
-TWO_GB = 2**30*2
-
-DEFAULT_DATA_TABLE_NAME = "bwa_mem_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
@@ -28,63 +26,66 @@
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 ):
- #TODO: allow multiple FASTA input files
- #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' )
+ # 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 )
if params['param_dict']['index_algorithm'] == 'automatic':
- if os.stat( fasta_filename ).st_size < TWO_GB: #use 2 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary
+ if os.stat( fasta_filename ).st_size < TWO_GB: # use 2 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 ]
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."
+ print("Error building index.", file=sys.stderr)
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' )
(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_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 )
-
- #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()
diff -r 414a92a973fa -r 46066df8813d data_manager/bwa_mem_index_builder.xml
--- a/data_manager/bwa_mem_index_builder.xml Thu Jan 19 11:48:36 2017 -0500
+++ b/data_manager/bwa_mem_index_builder.xml Tue Apr 04 18:07:04 2017 -0400
@@ -3,35 +3,34 @@
bwa
- bwa_mem_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 "bwa_mem_indexes"
-
-
-
-
+
-
-
-
+
+
+
-
-
-
-
+
+
+
-
-
.. 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.