diff data_manager/twobit_builder.py @ 3:5c77d4091880 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"

--- a/data_manager/twobit_builder.py	Tue Apr 04 18:16:29 2017 -0400
+++ b/data_manager/twobit_builder.py	Mon Nov 18 17:43:27 2019 -0500
@@ -12,7 +12,7 @@
 CHUNK_SIZE = 2**20  # 1mb
 
 
-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:
@@ -26,73 +26,73 @@
     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 )
+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" )
-    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+    args = ['faToTwoBit', fasta_filename, twobit_filename]
+    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("Error building index:", file=sys.stderr)
         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()
     # lastz_seqs
-    data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
+    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 )
+    _add_data_table_entry(data_manager_dict, "lastz_seqs", data_table_entry)
     # twobit.loc
-    data_table_entry = dict( value=sequence_id, path=twobit_base_name )
+    data_table_entry = dict(value=sequence_id, path=twobit_base_name)
 
-    _add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
+    _add_data_table_entry(data_manager_dict, "twobit", data_table_entry)
     # alignseq
-    data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
+    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 )
+    _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 )
+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('-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() )
+    params = loads(open(filename).read())
 
-    target_directory = params[ 'output_data' ][0]['extra_files_path']
-    os.mkdir( target_directory )
+    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_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
+    build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name)
 
     # save info to json file
-    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+    open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))
 
 
 if __name__ == "__main__":