Bio::Tools::EMBOSS::Palindrome(3pm) User Contributed Perl Documentation Bio::Tools::EMBOSS::Palindrome(3pm)
NAME
Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output
SYNOPSIS
# a simple script to turn palindrome output into GFF3
use Bio::Tools::EMBOSS::Palindrome;
use Bio::Tools::GFF;
my $parser = Bio::Tools::EMBOSS::Palindrome->new(-file => $filename);
my $out = Bio::Tools::GFF->new(-gff_version => 3,
-file => ">$filename.gff");
while( my $seq = $parser->next_seq ) {
for my $feat ( $seq->get_SeqFeatures ) {
$out->write_feature($feat);
}
}
DESCRIPTION
This is a parser for the EMBOSS tool 'palindrome'. It will produce a Bio::Seq object for each sequence analyzed. The sequence will be
empty (but will be of the correct length) and will have attached to it Bio::SeqFeature::FeaturePair objects which wil
FUTURE WORK
It may be consolidated into another framework at a later time, but for the time being it will stay a separate modules.
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via
email or the web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Tools::EMBOSS::Palindrome->new();
Function: Builds a new Bio::Tools::EMBOSS::Palindrome object
Returns : an instance of Bio::Tools::EMBOSS::Palindrome
Args : -file/-fh => a filename or filehandle for
initializing the parser
next_seq
Title : next_seq
Usage : my $seq = $parser->next_seq;
Function: Get the next feature set from the
Returns : L<Bio::SeqI> object
Args : none
source_tag
Title : source_tag
Usage : $obj->source_tag($newval)
Function: Get/Set Source Tag ('palindrome') by default
Returns : value of source_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::Tools::EMBOSS::Palindrome(3pm)