address #4 but needs refactoring

bretonics · May 5, 2017 · 7704ce0 · 7704ce0
1 parent 19df9ca
commit 7704ce0
Showing 1 changed file with 14 additions and 3 deletions.
diff --git a/Bioinformatics/Seq/Features.pm b/Bioinformatics/Seq/Features.pm
@@ -105,9 +105,11 @@ sub lookUpFeatures {
 # Save features to file
 sub _saveFeatures {
   my ($seqObj) = @_;
-  my @tags = qw(gene inference start end product protein_id translation);
-  my $strain  = $seqObj->display_id;
-  my $outFile = 'features_' . $strain . '.txt';
+  my @tags      = qw(gene locus_tag inference start end product protein_id translation);
+  my $strain    = $seqObj->display_id;
+  my $seq       = $seqObj->seq;
+  my $molecule  = $seqObj->molecule;
+  my $outFile   = 'features_' . $strain . '.txt';
   # $file =~ /(.+\/)?(.+)\..+/;
   my $FH      = getFH('>', $outFile);
 
@@ -130,6 +132,9 @@ sub _saveFeatures {
           $feat->has_tag($tag) ? print $FH $feat->get_tag_values($tag), "\t" : print $FH " \t" ;
         }
       }
+      # Handle translation if not protein file
+      my $translation = _translate() if($molecule eq 'PRT');
+      print $FH $translation;
       print $FH "\n"; # new line for each CDS
     }
   }
@@ -148,6 +153,12 @@ sub _printFeatures {
   }
 }
 
+sub _translate {
+  my ($seq) = @_;
+  say($seq->translate($seq));
+}
+
+
 =head1 COPYRIGHT AND LICENSE
 
 Andres Breton (C) 2017