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Bio::Coordinate::UtilsUser Contributed Perl DocumentaBio::Coordinate::Utils(3)

NAME
       Bio::Coordinate::Utils -	Additional methods to create Bio::Coordinate
       objects.

VERSION
       version 1.007001

SYNOPSIS
	   use Bio::Coordinate::Utils;
	   # get a Bio::Align::AlignI compliant	object,	$aln, somehow
	   # it	could be a Bio::SimpleAlign

	   $mapper = Bio::Coordinate::Utils->from_align($aln, 1);

	   # Build a set of mappers which will map, for	each sequence,
	   # that sequence position in the alignment (exon position to alignment
	   # position)
	   my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);

DESCRIPTION
       This class is a holder of methods that work on or create
       Bio::Coordinate::MapperI- compliant objects. . These methods are	not
       part of the Bio::Coordinate::MapperI interface and should in general
       not be essential	to the primary function	of sequence objects. If	you
       are thinking of adding essential	functions, it might be better to
       create your own sequence	class.	See Bio::PrimarySeqI, Bio::PrimarySeq,
       and Bio::Seq for	more.

METHODS
   new
       new() inherited from Root

   from_align
	Title	: from_align
	Usage	: $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
	Function:
		  Create a mapper out of an alignment.
		  The mapper will return a value only when both	ends of
		  the input range find a match.

		  Note:	This implementation works only on pairwise alignments
		  and is not yet well tested!

	Returns	: A Bio::Coordinate::MapperI
	Args	: Bio::Align::AlignI object
		  Id for the reference sequence, optional

   from_seq_to_alignmentpos
	Title	: from_seq_to_alignmentpos
	Usage	: $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
	Function:
		  Create a mapper out of an alignment.
		  The mapper will map the position of a	sequence into that position
		  in the alignment.

		  Will work on alignments of >=	2 sequences
	Returns	: An array of Bio::Coordinate::MapperI
	Args	: Bio::Align::AlignI object

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 the
       web:

	 https://github.com/bioperl/%%7Bdist%7D

AUTHORS
       Heikki Lehvaslaiho <heikki@bioperl.org>

       Jason Stajich <jason@bioperl.org>

COPYRIGHT
       This software is	copyright (c) by Heikki	Lehvaslaiho, and by Jason
       Stajich.

       This software is	available under	the same terms as the perl 5
       programming language system itself.

perl v5.24.1			  2016-12-15	     Bio::Coordinate::Utils(3)

NAME | VERSION | SYNOPSIS | DESCRIPTION | METHODS | FEEDBACK | AUTHORS | COPYRIGHT

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