diff data_manager/twobit_builder.py @ 0:74b09c8e5f6e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/twobit_builder.py	Thu Jun 11 16:14:27 2015 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys, os, tempfile, optparse, uuid, subprocess
+
+from json import loads, dumps
+
+
+CHUNK_SIZE = 2**20 #1mb
+
+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 #uuid.uuid4() generate and use an uuid
+    
+    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_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() )
+    return_code = proc.wait()
+    if return_code:
+        tmp_stderr.flush()
+        tmp_stderr.seek(0)
+        print >> sys.stderr, "Error building index:"
+        while True:
+            chunk = tmp_stderr.read( CHUNK_SIZE )
+            if not chunk:
+                break
+            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 )
+
+    _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 )
+
+    _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 )
+
+    _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 )
+    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' )
+    (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_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 ) )
+        
+if __name__ == "__main__": main()
+