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

[Jason Stajich]

done!

I added the ability to the update the primary,source,groupclass fields
using get/set methods as well. I also capitalized the 'Note' field to be
in line with the way GFF3 looks.

-j
On Mon, 15 Mar 2004, Cook, Malcolm wrote:

> 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;
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu