From f04eb986f3dc01ec4bc3e5c07a1431f470ea884c Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Wed, 5 Mar 2008 18:32:53 +0000 Subject: [PATCH] Turning off parsing of 'e' rows for MAF tools for now. e rows cause errors in bx-python when reversing, slicing, and writing (format_tabular). --- lib/galaxy/tools/util/maf_utilities.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/util/maf_utilities.py b/lib/galaxy/tools/util/maf_utilities.py index cca583ae553..9706ffdeab9 100644 --- a/lib/galaxy/tools/util/maf_utilities.py +++ b/lib/galaxy/tools/util/maf_utilities.py @@ -135,7 +135,7 @@ def maf_index_by_uid( maf_uid, index_location_file = None ): if maf_uid == fields[1]: try: maf_files = fields[3].replace( "\n", "" ).replace( "\r", "" ).split( "," ) - return bx.align.maf.MultiIndexed( maf_files, keep_open = True, parse_e_rows = True ) + return bx.align.maf.MultiIndexed( maf_files, keep_open = True, parse_e_rows = False ) except Exception, e: raise 'MAF UID (%s) found, but configuration appears to be malformed: %s' % ( maf_uid, e ) except: @@ -160,7 +160,7 @@ def build_maf_index( maf_file, species = None ): out = os.fdopen( fd, 'w' ) indexes.write( out ) out.close() - return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = True ), index_filename ) + return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = False ), index_filename ) except: return ( None, None )