bio::coordinate::utils(3pm) [debian man page]
Bio::Coordinate::Utils(3pm) User Contributed Perl Documentation Bio::Coordinate::Utils(3pm) 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 perl v5.14.2 2012-03-02 Bio::Coordinate::Utils(3pm)
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Bio::Coordinate::Result(3pm) User Contributed Perl Documentation Bio::Coordinate::Result(3pm) NAME
Bio::Coordinate::Result - Results from coordinate transformation SYNOPSIS
use Bio::Coordinate::Result; #get results from a Bio::Coordinate::MapperI $matched = $result->each_match; DESCRIPTION
The results from Bio::Coordinate::MapperI are kept in an object which itself is a split location, See Bio::Location::Split. The results are either Matches or Gaps. See Bio::Coordinate::Result::Match and Bio::Coordinate::Result::Gap. If only one Match is returned, there is a convenience method of retrieving it or accessing its methods. Same holds true for a Gap. 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 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 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ add_location Title : add_sub_Location Usage : $obj->add_sub_Location($variant) Function: Pushes one Bio::LocationI into the list of variants. Example : Returns : 1 when succeeds Args : Location object add_result Title : add_result Usage : $obj->add_result($result) Function: Adds the contents of one Bio::Coordinate::Result Example : Returns : 1 when succeeds Args : Result object seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to We override this here in order to propagate to all sublocations which are not remote (provided this root is not remote either) Returns : seq_id Args : [optional] seq_id value to set Convenience methods These methods are shortcuts to Match and Gap locations. each_gap Title : each_gap Usage : $obj->each_gap(); Function: Returns a list of Bio::Coordianate::Result::Gap objects. Returns : list of gaps Args : none each_match Title : each_match Usage : $obj->each_match(); Function: Returns a list of Bio::Coordinate::Result::Match objects. Returns : list of Matchs Args : none match Title : match Usage : $match_object = $obj->match(); #or $gstart = $obj->gap->start; Function: Read only method for retrieving or accessing the match object. Returns : one Bio::Coordinate::Result::Match Args : gap Title : gap Usage : $gap_object = $obj->gap(); #or $gstart = $obj->gap->start; Function: Read only method for retrieving or accessing the gap object. Returns : one Bio::Coordinate::Result::Gap Args : purge_gaps Title : purge_gaps Usage : $gap_count = $obj->purge_gaps; Function: remove all gaps from the Result Returns : count of removed gaps Args : perl v5.14.2 2012-03-02 Bio::Coordinate::Result(3pm)