lookup full filename

riyeyan · Nov 25, 2015 · 84961ad · 84961ad
1 parent c6d9bd1
commit 84961ad
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/dist.ini b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.5.2
+version = 3.5.3
 author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute

diff --git a/lib/Bio/Roary/AccessoryBinaryFasta.pm b/lib/Bio/Roary/AccessoryBinaryFasta.pm
@@ -78,7 +78,7 @@ sub create_accessory_binary_fasta {
 
             next if ( @files <= $self->_lower_bound_value || @files > $self->_upper_bound_value );
 
-            my $group_to_file_genes = $self->groups_to_files->{$group}->{$filename};
+            my $group_to_file_genes = $self->groups_to_files->{$group}->{$full_filename};
             if ( defined($group_to_file_genes) && @{$group_to_file_genes} > 0 ) {
                 $output_sequence .= 'A';
             }

diff --git a/t/Bio/Roary/CommandLine/Roary.t b/t/Bio/Roary/CommandLine/Roary.t
@@ -31,16 +31,16 @@ cleanup_files();
 
 %scripts_and_expected_files = (
 
-#   ' --dont_split_groups   t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
-#     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
-#   ' -j Local -t 1 --dont_split_groups   t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
-#     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
-#   ' -j Parallel  --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
-#     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
-#   ' -t 1 -j Parallel --dont_split_groups  t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
-#     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
-#   ' -j Local --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff' =>
-#     [ 'gene_presence_absence.csv', 't/data/genbank_gbff/genbank_gene_presence_absence.csv' ],
+   ' --dont_split_groups  ca   ' =>
+     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
+   ' -j Local -t 1 --dont_split_groups   t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
+     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
+   ' -j Parallel  --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
+     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
+   ' -t 1 -j Parallel --dont_split_groups  t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
+     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
+   ' -j Local --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff' =>
+     [ 'gene_presence_absence.csv', 't/data/genbank_gbff/genbank_gene_presence_absence.csv' ],
     '-h' => [ 'empty_file', 't/data/empty_file' ],
 );