Bio::SeqIO asciitree
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SeqIO::asciitree - asciitree sequence input/output stream
Package variables
No package variables defined.
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
_initialize
No description
Code
show_detailDescriptionCode
next_seqDescriptionCode
write_seqDescriptionCode
write_indented_sf
No description
Code
_locstr
No description
Code
Methods description
show_detailcode    nextTop
 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)
next_seqcodeprevnextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object (must be seq) to the stream
Returns : 1 for success and 0 for error
Args : array of 1 to n Bio::SeqI objects
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my($self,@args) = @_;

    $self->SUPER::_initialize(@args);
    # hash for functions for decoding keys.
}
show_detaildescriptionprevnextTop
sub show_detail {
    my $self = shift;

    return $self->{'show_detail'} = shift if @_;
    return $self->{'show_detail'};
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($self,@args) = @_;
    $self->throw("This is a WRITE-ONLY adapter");
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($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);
    }
}
write_indented_sfdescriptionprevnextTop
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;
}
_locstrdescriptionprevnextTop
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);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris MungallTop
Email cjm@fruitfly.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _