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

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

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.

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:

	 http://bugzilla.open-bio.org/

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

       Jason Stajich jason at bioperl.org

APPENDIX
       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a _

   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

perl v5.14.1			  2011-07-22	     Bio::Coordinate::Utils(3)
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