remove path from accessory tree

riyeyan · Nov 11, 2015 · adadb26 · adadb26
1 parent fd973fa
commit adadb26
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/dist.ini b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.4.2
+version = 3.4.3
 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
@@ -18,6 +18,7 @@ use Bio::Roary::AnnotateGroups;
 use Bio::Roary::AnalyseGroups;
 use Bio::Roary::Exceptions;
 use Bio::SeqIO;
+use File::Basename;
 
 has 'input_files'            => ( is => 'ro', isa => 'ArrayRef',                   required => 1 );
 has 'annotate_groups_obj'    => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
@@ -62,7 +63,9 @@ sub create_accessory_binary_fasta {
     my ($self) = @_;
     my $out_seq_io = Bio::SeqIO->new( -file => ">" . $self->output_filename, -format => 'Fasta' );
 
-    for my $filename ( @{ $self->input_files } ) {
+    for my $full_filename ( @{ $self->input_files } ) {
+        my($filename, $dirs, $suffix) = fileparse($full_filename);
+
         my $output_sequence = '';
         my $sample_name     = $filename;
         $sample_name =~ s!\.gff\.proteome\.faa!!;

diff --git a/t/Bio/Roary/AccessoryBinaryFasta.t b/t/Bio/Roary/AccessoryBinaryFasta.t
@@ -25,7 +25,7 @@ my $dummy_analyse_groups = Bio::Roary::AnalyseGroups->new(
 
 ok(
     my $obj = Bio::Roary::AccessoryBinaryFasta->new(
-        input_files => [ 'aaa', 'bbb', 'ccc', 'ddd' ],
+        input_files => [ 't/abc/aaa', 't/abc/bbb', 't/abc/ccc', 't/abc/ddd' ],
         groups_to_files => 
 		{
             group_1 => { 'aaa' => [1] },