diff data_manager/rnastar_index_builder.py @ 0:84f6e67cbae5 draft

Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rnastar_index_builder.py	Mon Sep 29 20:25:10 2014 -0400
@@ -0,0 +1,111 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+# adapted from Dan's BWA one for rna star
+# ross lazarus sept 2014
+#
+import sys
+import os
+import tempfile
+import optparse
+import subprocess
+
+from galaxy.util.json import from_json_string, to_json_string
+
+DEFAULT_DATA_TABLE_NAME = "rnastar_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_rnastar_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name,
+    sjdbOverhang,sjdbGTFfile, sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript,sjdbGTFfeatureExon,sjdbGTFchrPrefix,n_threads):
+    #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 )
+    pdict={'target_directory':target_directory,'n_threads':n_threads, 'sjdbFileChrStartEnd':sjdbFileChrStartEnd,
+           'sjdbGTFtagExonParentTranscript':sjdbGTFtagExonParentTranscript, 'sjdbGTFfeatureExon':sjdbGTFfeatureExon,
+           'sjdbGTFchrPrefix':sjdbGTFchrPrefix,'sjdbOverhang':sjdbOverhang, 'sjdbGTFfile':sjdbGTFfile,
+           'sym_linked_fasta_filename':sym_linked_fasta_filename}
+    
+    cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict
+    if sjdbGTFfile:
+         cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s
+   --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' %  pdict
+    elif sjdbFileChrStartEnd:
+        cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s'
+    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
+    args = cl.split(' ')
+    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: retcode=",retcode
+        while True:
+            chunk = tmp_stderr.read( CHUNK_SIZE )
+            if not chunk:
+                break
+            sys.stderr.write( chunk )
+    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 )
+
+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( '--out_file', default=None)
+    parser.add_option( '--out_index_path', default=None)
+    parser.add_option( '--sjdbGTFfile', type="string", default=None )
+    parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None )
+    parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None )
+    parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None )
+    parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None )
+    parser.add_option( '--sjdbOverhang', type="int", default=100 )
+    parser.add_option( '--runThreadN', type="int", default=4 )
+    (options, args) = parser.parse_args()
+    
+    filename = options.out_file
+    params = from_json_string( open( filename ).read() )
+    target_directory = options.out_index_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_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name,
+      sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile,
+      sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
+      sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix,
+      n_threads=options.runThreadN )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+        
+if __name__ == "__main__": main()