[Bioperl-l] Bio::Tools::EPCR.pm patch request

[Cook, Malcolm]

Jason,

I'd like it if you would accept and apply the following diff to the very
useful Bio::Tools::EPCR module.   I hope you agree that it provides more
flexibility in defining the structure of the features that are produced
(and, ultimately for me, the format of the GFF which gets written before
being loaded into Bio::DB::GFF database).

I have made the behaviour completely backwards compatible. 

Sincerely,

Malcolm Cook - mec at stowers-institute.org - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO  USA 

Index: EPCR.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v
retrieving revision 1.8
diff -c -r1.8 EPCR.pm
*** EPCR.pm	2002/12/01 00:05:21	1.8
--- EPCR.pm	2004/03/15 20:27:04
***************
*** 92,110 ****
  =head2 new
  
   Title   : new
!  Usage   : my $epcr = new Bio::Tools::EPCR(-file => $file);
!  Function: Initializes a new EPCR parser
   Returns : Bio::Tools::EPCR
   Args    : -fh   => filehandle
             OR
             -file => filename
  
  =cut
  
  sub new {
    my($class, at args) = @_;
  
    my $self = $class->SUPER::new(@args);
    $self->_initialize_io(@args);
    
    return $self;
--- 92,120 ----
  =head2 new
  
   Title   : new
!  Usage   : my $epcr = new Bio::Tools::EPCR(-file => $file, -primary =>
$fprimary, -source => $fsource, -groupclass => $fgroupclass);
!  Function: Initializes a new EPCR parser.  
   Returns : Bio::Tools::EPCR
   Args    : -fh   => filehandle
             OR
             -file => filename
  
+            -primary => a string to be used as the common value for
each features '-primary' tag.  Defaults to 'sts'.  (This in turn maps to
the GFF 'type' tag (aka 'method')).
+ 
+            -source => a string to be used as the common value for each
features '-source' tag.  Defaults to 'e-PCR'. (This in turn maps to the
GFF 'source' tag)
+ 
+            -groupclass => a string to be used as the name of the tag
which will hold the sts marker namefirst attribute.  Defaults to 'name'.
+ 
  =cut
  
  sub new {
    my($class, at args) = @_;
  
    my $self = $class->SUPER::new(@args);
+   my ($primary, $source, $groupclass) = $self->_rearrange([qw(PRIMARY
SOURCE GROUPCLASS)], at args);
+   $self->{'_primary'} = $primary || 'sts';
+   $self->{'_source'} =  $source || 'e-PCR';
+   $self->{'_groupclass'} =  $groupclass || 'name';
    $self->_initialize_io(@args);
    
    return $self;
***************
*** 139,152 ****
      my $markerfeature = new Bio::SeqFeature::Generic ( '-start'   =>
$start,
  						       '-end'     =>
$end,
  						       '-strand'  =>
$strand,
! 						       '-source'  =>
'e-PCR',
! 						       '-primary' =>
'sts',
  						       '-seq_id'  =>
$seqname,
  						       '-tag'     => {
! 							   'name'=>
$mkrname,
! 							   'note'=>
$rest,
  						       });
      return $markerfeature;
  }
  
  1;
--- 149,163 ----
      my $markerfeature = new Bio::SeqFeature::Generic ( '-start'   =>
$start,
  						       '-end'     =>
$end,
  						       '-strand'  =>
$strand,
! 						       '-source'  =>
$self->{'_source'},
! 						       '-primary' =>
$self->{'_primary'},
  						       '-seq_id'  =>
$seqname,
  						       '-tag'     => {
!
$self->{'_groupclass'}=> $mkrname,
  						       });
+     $markerfeature->add_tag_value('note',$rest) if $rest;
      return $markerfeature;
+ 
  }
  
  1;