diff data_manager/rnastar_index_builder.py @ 1:ebadd2c92958 draft

Uploaded

--- a/data_manager/rnastar_index_builder.py	Mon Sep 29 20:25:10 2014 -0400
+++ b/data_manager/rnastar_index_builder.py	Mon Sep 29 20:47:45 2014 -0400
@@ -43,7 +43,7 @@
          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'
+        cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
     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() )
@@ -104,6 +104,7 @@
       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 ) )