[Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phast PhastCons.pm, 1.4, 1.5

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Jan 30 11:39:44 EST 2007


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phast
In directory dev.open-bio.org:/tmp/cvs-serv2591/Bio/Tools/Run/Phylo/Phast

Modified Files:
	PhastCons.pm 
Log Message:
added a predicted tag to each result, corrected coords

Index: PhastCons.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phast/PhastCons.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** PhastCons.pm	25 Jan 2007 15:41:40 -0000	1.4
--- PhastCons.pm	30 Jan 2007 16:39:42 -0000	1.5
***************
*** 122,125 ****
--- 122,126 ----
  use Bio::Tools::Run::Phylo::Phast::PhyloFit;
  use Bio::FeatureIO;
+ use Bio::Annotation::SimpleValue;
  
  use base qw(Bio::Tools::Run::Phylo::PhyloBase);
***************
*** 382,390 ****
      while (my $feat = $bedin->next_feature) {
          $feat->source('phastCons');
          
!         # features are in alignment coords; make a feature for each alignment
!         # sequence
          foreach my $seq ($aln->each_seq) {
              my $clone = clone($feat);
              
              # give it the correct id
--- 383,395 ----
      while (my $feat = $bedin->next_feature) {
          $feat->source('phastCons');
+         my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1);
+         $feat->annotation->add_Annotation($sv);
+         # $feat->type('TF_binding_site'); causes seg fault in subsequent clone()
          
!         # features are in zero-based alignment coords; make a feature for each
!         # alignment sequence
          foreach my $seq ($aln->each_seq) {
              my $clone = clone($feat);
+             # $clone->type('TF_binding_site'); causes massive slowdown if you later store/retrieve these features from Bio::DB::SeqFeature database
              
              # give it the correct id
***************
*** 392,397 ****
              
              # correct the coords
!             $clone->start($seq->location_from_column($feat->start)->start);
!             $clone->end($seq->location_from_column($feat->end)->end);
              
              push(@feats, $clone);
--- 397,402 ----
              
              # correct the coords
!             $clone->start($seq->location_from_column($feat->start + 1)->start);
!             $clone->end($seq->location_from_column($feat->end + 1)->end);
              
              push(@feats, $clone);



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