Summary

Bio::SeqIO::asciitree - asciitree sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

  # It is probably best not to use this object directly, but
  # rather go through the SeqIO handler system. Go:

    $instream  = Bio::SeqIO->new(-file => $filename,
                                 -format => 'chadoxml');
    $outstream = Bio::SeqIO->new(-file => $filename,
                                 -format => 'asciitree');

    while ( my $seq = $instream->next_seq() ) {
	$outstream->write_seq();
    }

Description

This is a WRITE-ONLY SeqIO module. It writes a Bio::SeqI object
containing nested SeqFeature objects in such a way that the SeqFeature
containment hierarchy is visible as a tree structure

Methods

Methods description

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

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object (must be seq) to the stream
 Returns : 1 for success and 0 for error
 Args    : array of 1 to n Bio::SeqI objects

Methods code

sub _initialize {

    my($self,@args) = @_;
    
    $self->SUPER::_initialize(@args); 
    # hash for functions for decoding keys.

}

sub show_detail {

    my $self = shift;

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

}

sub next_seq {

    my ($self,@args) = @_;
    $self->throw("This is a WRITE-ONLY adapter");

}

sub write_seq {

    my ($self,@seqs) = @_;

    foreach my $seq ( @seqs ) {
	$self->throw("Attempting to write with no seq!") unless defined $seq;

	if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) {
	    $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!");
	}
	$self->_print("Seq: ".$seq->accession_number);
	$self->_print("\n");
	my @top_sfs = $seq->get_SeqFeatures;
	$self->write_indented_sf(1, @top_sfs);
    }

}

sub write_indented_sf {

    my $self = shift;
    my $indent = shift;
    my @sfs = @_;
    foreach my $sf (@sfs) {
        my $label = '';
        if ($sf->has_tag('standard_name')) {
            ($label) = $sf->get_tag_values('standard_name');
        }
        if ($sf->has_tag('product')) {
            ($label) = $sf->get_tag_values('product');
        }
	my $COLS = 60;
	my $tab = ' ' x 10;
	my @lines = ();
	if ($self->show_detail) {
	    my @tags = $sf->all_tags;
	    foreach my $tag (@tags) {
		my @vals = $sf->get_tag_values($tag);
		foreach my $val (@vals) {
		    $val = "\"$val\"";
		    push(@lines, 
			 "$tab/$tag=");
		    while (my $cut = 
			   substr($val, 0, $COLS - length($lines[-1]), '')) {
			$lines[-1] .= "$cut";
			if ($val) {
			    push(@lines, $tab);
			}
		    }
		}
	    }
	}
	my $detail = join("\n", @lines);
	
        my @sub_sfs = $sf->get_SeqFeatures;
	my $locstr = '';
	if (!@sub_sfs) {
	    $locstr = $self->_locstr($sf);
	}
        my $col1 = sprintf("%s%s $label", 
			   '  ' x $indent, $sf->primary_tag);
	my $line = sprintf("%-50s %s\n",
			   substr($col1, 0, 50), $locstr);
	$self->_print($line);
	if ($detail) {
	    $self->_print($detail."\n");
	}
	$self->write_indented_sf($indent+1, @sub_sfs);
    }
    return;

}

sub _locstr {

    my $self = shift;
    my $sf = shift;
    my $strand = $sf->strand || 0;
    my $ss = '.';
    $ss = '+' if $strand > 0;
    $ss = '-' if $strand < 0;

    my $splitlocstr = '';
    if ($sf->isa("Bio::SeqFeatureI")) {
        my @locs = ($sf->location);
        if ($sf->location->isa("Bio::Location::SplitLocationI")) {
            @locs = $sf->location->each_Location;
            $splitlocstr = "; SPLIT: ".join(" ", 
                                          map {$self->_locstr($_)} @locs);
            
        }
    }
    
    return
      sprintf("%d..%d[%s] $splitlocstr", $sf->start, $sf->end, $ss);

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://www.bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email cjm@fruitfly.org

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