# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent kpvincent@bx.psu.edu # Date 1283231072 14400 # Node ID b7e13932acf9e58dee2bb3f2799e7e27402ffc63 # Parent 1cd9009036f729c8d36fe40db6cbfd6508c3a635 Issue #380: Properly handle -n and -v options in Bowtie

--- a/tools/sr_mapping/bowtie_wrapper.py +++ b/tools/sr_mapping/bowtie_wrapper.py @@ -120,6 +120,7 @@ def __main__(): parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) (options, args) = parser.parse_args() stdout = '' + # make temp directory for placement of indices and copy reference file there if necessary tmp_index_dir = tempfile.mkdtemp() # get type of data (solid or solexa) @@ -190,7 +191,7 @@ def __main__(): # clean up temp dir if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) - stop_err( 'Something is wrong with the indexing parameters and the indexing and alignment could not be run\n' + str( e ) ) + stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) ) ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() @@ -259,7 +260,7 @@ def __main__(): trimL = '-3 %s' % options.trimL else: trimL = '' - if options. mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ + if options.mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ or options.mismatchSeed == '2' or options.mismatchSeed == '3'): mismatchSeed = '-n %s' % options.mismatchSeed else: @@ -276,7 +277,7 @@ def __main__(): rounding = '--nomaqround' else: rounding = '' - if options.maqSoapAlign != '-1': + if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0: maqSoapAlign = '-v %s' % options.maqSoapAlign else: maqSoapAlign = ''