diff data_manager/data_manager_sam_fasta_index_builder.py @ 5:cc4ef4d38cf9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"

--- a/data_manager/data_manager_sam_fasta_index_builder.py	Thu Sep 14 15:30:56 2017 -0400
+++ b/data_manager/data_manager_sam_fasta_index_builder.py	Mon Nov 18 15:07:34 2019 -0500
@@ -13,7 +13,7 @@
 DEFAULT_DATA_TABLE_NAME = "fasta_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:
@@ -27,65 +27,73 @@
     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 ):
+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
-    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 )
+    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 )
+    args = ['samtools', 'faidx']
+    args.append(sym_linked_fasta_filename)
     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() )
+    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 )
-        sys.stderr.write( "Error building index:\n" )
+        tmp_stderr.seek(0)
+        sys.stderr.write("Error building index:\n")
         while True:
-            chunk = tmp_stderr.read( CHUNK_SIZE )
+            chunk = tmp_stderr.read(CHUNK_SIZE)
             if not chunk:
                 break
-            sys.stderr.write( chunk )
-        sys.exit( return_code )
+            sys.stderr.write(chunk)
+        sys.exit(return_code)
     tmp_stderr.close()
-    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 )
+    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 )
+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='store', 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='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 )
+    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 ) )
+    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 )
+    sequence_id, sequence_name = get_id_name(params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description)
 
     # 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 )
+    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
-    open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
+    open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
 
 
 if __name__ == "__main__":