NAME

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

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

FEEDBACK

Mailing Lists

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

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 Bugs

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Mungall

Email cjm@fruitfly.org

APPENDIX

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

show_detail

 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_seq

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

write_seq

 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