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