Provided by: libbio-coordinate-perl_1.7.1-3_all
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.
new new() inherited from Root 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
Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. firstname.lastname@example.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: email@example.com 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/%%7Bdist%7D
Heikki Lehvaslaiho <firstname.lastname@example.org> Jason Stajich <email@example.com>
This software is copyright (c) by Heikki Lehvaslaiho, and by Jason Stajich. This software is available under the same terms as the perl 5 programming language system itself.