Summary

Bio::FeatureIO::bed - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::FeatureIO

Synopsis

Give standard usage here

Description

http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED

Methods

Methods description

 Title   : _initialize
 Function: initializes BED for reading/writing (currently write-only)
 Args    : all optional:
           name          description
           ----------------------------------------------------------
           -name         the name for the BED track, stored in header
                         name defaults to localtime()
           -description  the description for the BED track, stored in
                         header.  defaults to localtime().
           -use_score    whether or not the score attribute of
                         features should be used when rendering them.
                         the higher the score the darker the color.
                         defaults to 0 (false)

 Title   : use_score
 Usage   : $obj->use_score($newval)
 Function: should score be used to adjust feature color when rendering?  set to true if so.
 Example : 
 Returns : value of use_score (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

 Title   : name
 Usage   : $obj->name($newval)
 Function: name of BED track
 Example : 
 Returns : value of name (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

 Title   : description
 Usage   : $obj->description($newval)
 Function: description of BED track
 Example : 
 Returns : value of description (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

Methods code

sub _initialize {

  my($self,%arg) = @_;

  $self->SUPER::_initialize(%arg);

  $self->name($arg{-name} || scalar(localtime()));
  $self->description($arg{-description} || scalar(localtime()));
  $self->use_score($arg{-use_score} || 0);

  $self->_print(sprintf('track name="%s" description="%s" useScore=%d',
                        $self->name,
                        $self->description,
                        $self->use_score ? 1 : 0
                       )
               );

}

sub use_score {

    my $self = shift;

    return $self->{'use_score'} = shift if @_;
    return $self->{'use_score'};

}

sub name {

    my $self = shift;

    return $self->{'name'} = shift if @_;
    return $self->{'name'};

}

sub description {

    my $self = shift;

    return $self->{'description'} = shift if @_;
    return $self->{'description'};

}

sub write_feature {

  my($self,$feature) = @_;
  $self->throw("only Bio::SeqFeature::Annotated objects are writeable") unless $feature->isa('Bio::SeqFeature::Annotated');

  my $chrom       = $feature->seq_id || '';
  my $chrom_start = $feature->start  || 0;
  my $chrom_end   = $feature->stop   || 0;

  #try to make a reasonable name
  my $name        = undef;
  if(my @v = ($feature->annotation->get_Annotations('Name'))){
    $name = $v[0];
    $self->warn("only using first of feature's multiple names: ".join ',', map {$_->value} @v) if scalar(@v) > 1;
  } elsif(my @v = ($feature->annotation->get_Annotations('ID'))){
    $name = $v[0];
    $self->warn("only using first of feature's multiple IDs: ".join ',', map {$_->value} @v) if scalar(@v) > 1;
  } else {
    $name = 'anonymous';
  }

  my $score = $feature->score || 0;
  my $strand = $feature->strand == 0 ? '-' : '+'; #default to +
  my $thick_start = '';  #not implemented, used for CDS
  my $thick_end = '';    #not implemented, used for CDS
  my $reserved = 0;
  my $block_count = '';  #not implemented, used for sub features
  my $block_sizes = '';  #not implemented, used for sub features
  my $block_starts = ''; #not implemented, used for sub features

  $self->_print(join("\t",($chrom,$chrom_start,$chrom_end,$name,$score,$strand,$thick_start,$thick_end,$reserved,$block_count,$block_sizes, $block_starts)));
  $self->write_feature($_) foreach $feature->get_SeqFeatures();

}

sub next_feature {

  shift->throw_not_implemented();

}

General documentation

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Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _