Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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


     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);


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.


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Please direct usage questions or support issues to the mailing list:

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:

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

Jason Stajich jason at


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


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


  Title   : from_seq_to_alignmentpos
  Usage   : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
            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