From 49a0fcc92f01ccb69f4bc9b9c6d4124c0060c0de Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Tue, 15 Dec 2009 19:18:22 -0500 Subject: [PATCH] fix for parsing blastdb.loc for the megablast wrapper tool --- tools/metag_tools/megablast_wrapper.py | 5 ++--- tools/metag_tools/megablast_wrapper.xml | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper.py index e5aa7b33656..96d7d47dd30 100644 --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -30,7 +30,7 @@ def __main__(): #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 @@ def __main__(): 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 --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml index ab6017798c8..b33cfd847d3 100644 --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -2,7 +2,7 @@ compare short reads against htgs, nt, and wgs databases megablast_wrapper.py - --db_build=$source_select + --db_build="$source_select" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff