/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Coordinate::Utils

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