Merge pull request #3 from andrewjpage/master

genus
sanger-pathogens · Apr 2, 2013 · 8ce8989 · 8ce8989
2 parents 0d4a0c9 + 4936d2a
commit 8ce8989
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/lib/Bio/AutomatedAnnotation.pm b/lib/Bio/AutomatedAnnotation.pm
@@ -1,5 +1,4 @@
 package Bio::AutomatedAnnotation;
-
 # ABSTRACT: Automated annotation of assemblies
 
 =head1 SYNOPSIS
@@ -31,6 +30,7 @@ has 'annotation_tool'   => ( is => 'ro', isa => 'Str', default  => 'Prokka' );
 has 'outdir'            => ( is => 'ro', isa => 'Str', default  => 'annotation' );
 has 'tmp_directory'     => ( is => 'ro', isa => 'Str', default  => '/tmp' );
 has 'sequencing_centre' => ( is => 'ro', isa => 'Str', default  => 'SC' );
+has 'genus'             => ( is => 'ro', isa => 'Maybe[Str]' );
 has 'accession_number'  => ( is => 'ro', isa => 'Maybe[Str]' );
 
 has '_annotation_pipeline_class' =>
@@ -72,6 +72,13 @@ sub annotate {
         force          => 1,
         contig_uniq_id => $self->_contig_uniq_id
     );
+
+    if(defined($self->genus))
+    {
+      $annotation_pipeline->genus($self->genus);
+      $annotation_pipeline->usegenus(1);
+    }
+
     $annotation_pipeline->annotate;
 
     chdir($original_cwd);

diff --git a/lib/Bio/AutomatedAnnotation/Prokka.pm b/lib/Bio/AutomatedAnnotation/Prokka.pm
@@ -57,19 +57,19 @@ has 'locustag'        => ( is => 'ro', isa => 'Str',  lazy    => 1, builder => '
 has 'increment'       => ( is => 'ro', isa => 'Int',  default => 1 );
 has 'gffver'          => ( is => 'ro', isa => 'Int',  default => 3 );
 has 'centre'          => ( is => 'ro', isa => 'Str',  default => 'VBC' );
-has 'genus'           => ( is => 'ro', isa => 'Str',  default => 'Genus' );
+has 'genus'           => ( is => 'rw', isa => 'Str',  default => 'Genus' );
 has 'species'         => ( is => 'ro', isa => 'Str',  default => 'species' );
 has 'strain'          => ( is => 'ro', isa => 'Str',  default => 'strain' );
 has 'contig_uniq_id'  => ( is => 'ro', isa => 'Str',  default => 'gnl' );
 has 'kingdom'         => ( is => 'ro', isa => 'Str',  default => 'Bacteria' );
 has 'gcode'           => ( is => 'ro', isa => 'Int',  default => 0 );
 has 'gram'            => ( is => 'ro', isa => 'Str',  default => '' );
-has 'usegenus'        => ( is => 'ro', isa => 'Bool', default => 0 );
+has 'usegenus'        => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'proteins'        => ( is => 'ro', isa => 'Str',  default => '' );
 has 'fast'            => ( is => 'ro', isa => 'Bool', default => 0 );
 has 'cpus'            => ( is => 'ro', isa => 'Int',  default => 0 );
 has 'mincontig'       => ( is => 'ro', isa => 'Int',  default => 200 );
-has 'evalue'          => ( is => 'ro', isa => 'Num',  default =>   );
+has 'evalue'          => ( is => 'ro', isa => 'Num',  default => 1E-6 );
 has 'rfam'            => ( is => 'ro', isa => 'Bool', default => 0 );
 has 'files_per_chunk' => ( is => 'ro', isa => 'Int',  default => 10 );
 has 'tempdir'         => ( is => 'ro', isa => 'Str',  default => '/tmp' );