details: http://www.bx.psu.edu/hg/galaxy/rev/e905ef22c648 changeset: 3181:e905ef22c648 user: Nate Coraor nate@bx.psu.edu date: Tue Dec 15 19:18:22 2009 -0500 description: fix for parsing blastdb.loc for the megablast wrapper tool

diffstat:

tools/metag_tools/megablast_wrapper.py | 5 ++--- tools/metag_tools/megablast_wrapper.xml | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-)

diffs (34 lines):

diff -r 362126943cd7 -r e905ef22c648 tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Tue Dec 15 15:58:24 2009 -0500 +++ b/tools/metag_tools/megablast_wrapper.py Tue Dec 15 19:18:22 2009 -0500 @@ -30,7 +30,7 @@ #Parse Command Line options, args = doc_optparse.parse( __doc__ )

- db_build = options.db_build.split( ' ' )[0] + db_build = options.db_build query_filename = options.input.strip() output_filename = options.output.strip() mega_word_size = options.word_size # -W @@ -62,8 +62,7 @@ if not line or line.startswith( '#' ): continue fields = line.split( '\t' ) - if len( fields ) == 2: - db[ fields[0].split( ' ' )[0] ] = fields[1] + db[ fields[0] ] = fields[1]

if not db.has_key( db_build ): stop_err( 'Cannot locate the target database. Please check your location file.' ) diff -r 362126943cd7 -r e905ef22c648 tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml Tue Dec 15 15:58:24 2009 -0500 +++ b/tools/metag_tools/megablast_wrapper.xml Tue Dec 15 19:18:22 2009 -0500 @@ -2,7 +2,7 @@ <description> compare short reads against htgs, nt, and wgs databases</description> <command interpreter="python"> megablast_wrapper.py - --db_build=$source_select + --db_build="$source_select" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff