[Bioperl-guts-l] bioperl-live/Bio/Tools Infernal.pm,1.2,1.3

Christopher John Fields cjfields at dev.open-bio.org
Sun Jan 7 17:36:07 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory dev.open-bio.org:/tmp/cvs-serv11698

Modified Files:
	Infernal.pm 
Log Message:
small changes

Index: Infernal.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Infernal.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Infernal.pm	13 Dec 2006 22:40:42 -0000	1.2
--- Infernal.pm	7 Jan 2007 22:36:05 -0000	1.3
***************
*** 49,63 ****
  Model data is accessible via the following:
    
!   Data            SeqFeature::FeaturePair     Note
!   ------------------------------------------------------------------
!   start           $sf->start
!   end             $sf->end
!   score(bits)     $sf->score
!   strand          $sf->strand
!   seqid           $sf->seq_id
  
  Hit data is accessible via the following:
  
!   Data            SeqFeature::FeaturePair     Note
    ------------------------------------------------------------------
    start           $sf->hstart
--- 49,66 ----
  Model data is accessible via the following:
    
!   Data            SeqFeature::FeaturePair         Note
!   --------------------------------------------------------------------------
!   primary tag     $sf->primary_tag                Rfam ID (if passed to new())
!   start           $sf->start                      Based on CM length
!   end             $sf->end                        Based on CM length
!   score           $sf->score                      Bit score
!   strand          $sf->strand                     0 (CM does not have a strand)
!   seqid           $sf->seq_id                     Rfam ID (if passed to new())
!   display name    $sf->feature1->display_name     CM name (if passed to new())
!   source          $sf->feature1->source tag      'Infernal' followed by version
  
  Hit data is accessible via the following:
  
!   Data            SeqFeature::FeaturePair         Note
    ------------------------------------------------------------------
    start           $sf->hstart
***************
*** 69,72 ****
--- 72,88 ----
    Source Tag      $sf->hsource_tag
  
+ primary_tag => $mt,
+ 
+                 my $hf = Bio::SeqFeature::Generic->new( -primary_tag => $mt,
+                               -source_tag  => "$st $ver",
+                               -display_name => $dt || '',
+                               -score       => $score,
+                               -start       => $start,
+                               -end         => $end,
+                               -seq_id      => $qid,
+                               -strand      => $strand
+                             );
+ 
+ 
  Added FeaturePair tags are : 
  
***************
*** 146,152 ****
             -minscore  - minimum score (simple screener, since Infernal generates
                          a ton of spurious hits)
  =cut
  
! # yes, this is actually initialize, but the args need to be passed to new
  # see Bio::Tools::AnalysisResult for further details
  
--- 162,170 ----
             -minscore  - minimum score (simple screener, since Infernal generates
                          a ton of spurious hits)
+            -version   - Infernal program version
  =cut
  
! # yes, this is actually _initialize, but the args are passed to
! # the constructor.
  # see Bio::Tools::AnalysisResult for further details
  
***************
*** 168,175 ****
    $cm        && $self->covariance_model($cm);
    $rfam      && $self->rfam($rfam);
!   $ver ||= $DEFAULT_VERSION;
!   $self->program_version($ver);
!   $ms ||= $MINSCORE;
!   $self->minscore($ms);
  }
  
--- 186,191 ----
    $cm        && $self->covariance_model($cm);
    $rfam      && $self->rfam($rfam);
!   $self->program_version(defined $ver ? $ver : $DEFAULT_VERSION);
!   $self->minscore(defined $ms ? $ms : $MINSCORE);
  }
  
***************
*** 219,223 ****
  }
  
- 
  =head2 desc_tag
  
--- 235,238 ----



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