Bio::SeqIO::asciitree(User Contributed Perl DocumentatBio::SeqIO::asciitree(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::SeqIO::asciitree(3)
