Bio::Coordinate::Utils.3pm

Langue: en

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

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
 
 

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