details: http://www.bx.psu.edu/hg/galaxy/rev/fbd7d0a0f596 changeset: 2756:fbd7d0a0f596 user: Dan Blankenberg dan@bx.psu.edu date: Wed Sep 23 17:01:04 2009 -0400 description: Two MAF related bug fixes.
2 file(s) affected in this change:
lib/galaxy/datatypes/sequence.py lib/galaxy/tools/util/maf_utilities.py
diffs (23 lines):
diff -r 69615210cf99 -r fbd7d0a0f596 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Wed Sep 23 13:25:22 2009 -0400 +++ b/lib/galaxy/datatypes/sequence.py Wed Sep 23 17:01:04 2009 -0400 @@ -406,6 +406,7 @@ """ #these metadata values are not accessable by users, always overwrite indexes, species, species_chromosomes = COPIED_build_maf_index_species_chromosomes( dataset.file_name ) + if indexes is None: return #this is not a MAF file
dataset.metadata.species = species #only overwrite the contents if our newly determined chromosomes don't match stored diff -r 69615210cf99 -r fbd7d0a0f596 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Wed Sep 23 13:25:22 2009 -0400 +++ b/lib/galaxy/tools/util/maf_utilities.py Wed Sep 23 17:01:04 2009 -0400 @@ -504,7 +504,7 @@
def get_species_in_maf( maf_filename ): species = [] - for block in maf.Reader( open( maf_filename ) ): + for block in bx.align.maf.Reader( open( maf_filename ) ): for spec in get_species_in_block( block ): if spec not in species: species.append( spec )