Implement write_feature() in FeatureIO::ptt

bioperl · Jun 22, 2011 · 29f1f4b · 29f1f4b
1 parent 2d0c41b
commit 29f1f4b
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Showing 2 changed files with 37 additions and 5 deletions.
diff --git a/Bio/FeatureIO/ptt.pm b/Bio/FeatureIO/ptt.pm
@@ -190,19 +190,51 @@ sub next_feature {
   return $feat;
 }
 
-=head2 write_feature (NOT IMPLEMENTED)
+=head2 write_feature
 
  Title   : write_feature
  Usage   : $io->write_feature($feature)
- Function: write a Bio::SeqFeatureI object in PTT format
+ Function: write a Bio::SeqFeature object in PTT format with no header
  Example : 
- Args    : Bio::SeqFeatureI object
+ Args    : Bio::SeqFeature object
  Returns : 
 
 =cut
 
 sub write_feature {
-  shift->throw_not_implemented;
+  my($self,$feat) = @_;
+
+  # Example, with header:
+  # Location  Strand  Length  PID Gene  Synonym Code  COG Product
+  # 190..255  + 21  16763391  thrL  STM0001 - - thr operon leader peptide
+
+  $self->throw("Only Bio::SeqFeature::Generic or Bio::SeqFeature::Annotated objects are writeable") 
+  unless ( $feat->isa('Bio::SeqFeature::Generic') || $feat->isa('Bio::SeqFeature::Annotated') );
+
+  # Could be a problematic condition since it assumes all proteins have a 
+  # primary tag of 'CDS' as in the Genbank files from NCBI
+  if ( $feat->primary_tag eq 'CDS' ) {
+
+    # Default
+    my ($len,$pid,$gene,$synonym,$code,$cog,$product) = qw(- - - - - - -);
+
+    my $start = $feat->start;
+    my $end   = $feat->end;
+    my $loc   = "$start..$end";
+
+    my $strand = $feat->strand == 1 ? '+' : '-';
+
+    $len = int(($end - $start)/3);
+
+    $product = join ' ',$feat->get_tag_values("product")     if ($feat->has_tag("product"));
+    $pid     = join ' ',$feat->get_tag_values("protein_id")  if ($feat->has_tag("protein_id"));
+    $code    = join ' ',$feat->get_tag_values("codon_start") if ($feat->has_tag("codon_start"));
+
+    $self->_print(join("\t",($loc,$strand,$len,$pid,$gene,$synonym,$code,$cog,$product)) . "\n");
+
+    $self->write_feature($_) foreach $feat->get_SeqFeatures();
+
+  }
 }
 
 =head2 description

diff --git a/t/SeqFeature/FeatureIO.t b/t/SeqFeature/FeatureIO.t
@@ -203,7 +203,7 @@ is($f->seq_id, "chr1");
 
 ################################################################################
 #
-# use FeatureIO::gff to read a PTT file.
+# use FeatureIO::ptt to read a PTT file.
 #
 $fcount = 0;