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