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#
# BioPerl module for Bio::Tools::EPCR
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 72 lines of Pod
=head1 NAME
Bio::Tools::EPCR - Parse ePCR output and make features
=head1 SYNOPSIS
    # A simple annotation pipeline wrapper for ePCR data
    # assuming ePCR data is already generated in file seq1.epcr
    # and sequence data is in fasta format in file called seq1.fa
    use Bio::Tools::EPCR;
    use Bio::SeqIO;
    my $parser = Bio::Tools::EPCR->new(-file => 'seq1.epcr');
    my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa');
    my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");
    while( my $feat = $parser->next_feature ) {
        # add EPCR annotation to a sequence
        $seq->add_SeqFeature($feat);
    }
    my $seqout = Bio::SeqIO->new(-format => 'embl');
    $seqout->write_seq($seq);
=head1 DESCRIPTION
This object serves as a parser for ePCR data, creating a
Bio::SeqFeatureI for each ePCR hit.  These can be processed or added
as annotation to an existing Bio::SeqI object for the purposes of
automated annotation.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Support 
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::EPCR;
$Bio::Tools::EPCR::VERSION = '1.7.8';
use strict;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
HideShow 29 lines of Pod
=head2 new
 Title   : new
 Usage   : my $epcr = Bio::Tools::EPCR->new(-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,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my ($primary, $source, 
      $groupclass) = $self->_rearrange([qw(PRIMARY
                                           SOURCE 
                                           GROUPCLASS)],@args);
  $self->primary(defined $primary ? $primary : 'sts');
  $self->source(defined $source ? $source : 'e-PCR');
  $self->groupclass(defined $groupclass ? $groupclass : 'name');
  $self->_initialize_io(@args);
  return $self;
}
HideShow 13 lines of Pod
=head2 next_feature
 Title   : next_feature
 Usage   : $seqfeature = $obj->next_feature();
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none    
=cut
sub next_feature {
    my ($self) = @_;
    my $line = $self->_readline;
    return unless defined($line);
    chomp($line);
    my($seqname,$location,$mkrname, $rest) = split(/\s+/,$line,4);
     
    my ($start,$end) = ($location =~ /(\S+)\.\.(\S+)/);
    # `e-PCR -direct` results code match strand in $rest as (+) and (-).  Decode it if present.
    my $strandsign;
    if ($rest =~ m/^\(([+-])\)(.*)$/) {
      ($strandsign,$rest) = ($1, $2);
    } else {
      $strandsign = "?";
    }
    my $strand = $strandsign eq "+" ? 1 :  $strandsign eq "-" ? -1 : 0;
    my $markerfeature = Bio::SeqFeature::Generic->new 
        ( '-start'   => $start,
          '-end'     => $end,
          '-strand'  => $strand,
          '-source'  => $self->source,
          '-primary' => $self->primary,
          '-seq_id'  => $seqname,
          '-tag'     => {
              $self->groupclass => $mkrname,
              ($rest ? ('Note'            => $rest ) : ()),
          });
    #$markerfeature->add_tag_value('Note', $rest) if defined $rest;
    return $markerfeature;
}
HideShow 12 lines of Pod
=head2 source
 Title   : source
 Usage   : $obj->source($newval)
 Function: 
 Example : 
 Returns : value of source (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub source{
    my $self = shift;
    return $self->{'_source'} = shift if @_;
    return $self->{'_source'};
}
HideShow 12 lines of Pod
=head2 primary
 Title   : primary
 Usage   : $obj->primary($newval)
 Function: 
 Example : 
 Returns : value of primary (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub primary{
    my $self = shift;
    return $self->{'_primary'} = shift if @_;
    return $self->{'_primary'};
}
HideShow 12 lines of Pod
=head2 groupclass
 Title   : groupclass
 Usage   : $obj->groupclass($newval)
 Function: 
 Example : 
 Returns : value of groupclass (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub groupclass{
    my $self = shift;
    return $self->{'_groupclass'} = shift if @_;
    return $self->{'_groupclass'};
}
1;