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:

  https://redmine.open-bio.org/projects/bioperl/

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