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Bio::Tools::EMBOSS::PaUserrContributed Perl DBio::Tools::EMBOSS::Palindrome(3)

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)

perl v5.32.1			  2019-12-07 Bio::Tools::EMBOSS::Palindrome(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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