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Turning off parsing of 'e' rows for MAF tools for now.

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e rows cause errors in bx-python when reversing, slicing, and writing (format_tabular).
This commit is contained in:
Daniel Blankenberg
2008-03-05 18:32:53 +00:00
parent 9863127799
commit f04eb986f3
1 changed files with 2 additions and 2 deletions
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lib/galaxy/tools/util/maf_utilities.py
+2 -2
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@@ -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 )