[hg] galaxy 1491: Fix for GMAJ tool when species chromosomes are...

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[hg] galaxy 1491: Fix for GMAJ tool when species chromosomes are...

greg
details:   http://www.bx.psu.edu/hg/galaxy/rev/9b8d06eea5b7
changeset: 1491:9b8d06eea5b7
user:      Dan Blankenberg <[hidden email]>
date:      Wed Sep 03 12:06:33 2008 -0400
description:
Fix for GMAJ tool when species chromosomes are not specified. Error appears in paster.log as 'TypeError: iterable argument required'

1 file(s) affected in this change:

tools/visualization/GMAJ.xml

diffs (12 lines):

diff -r cefbb71490a2 -r 9b8d06eea5b7 tools/visualization/GMAJ.xml
--- a/tools/visualization/GMAJ.xml Sun Aug 31 21:14:06 2008 -0400
+++ b/tools/visualization/GMAJ.xml Wed Sep 03 12:06:33 2008 -0400
@@ -82,7 +82,7 @@
 
 #set $seq_count = 0
 #for $spec_count, $annotation in $enumerate( $annotations ):
-#if $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]:
+#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]:
 #set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]]
 #else
 #set $seq_names = [$annotation['species'].value]