NAME

CracTools::Annotator - Generic annotation base on CracTools::GFF::Query

VERSION

version 1.08

METHODS

new

  Arg [1] : String - $gff_file
            GFF file to perform annotation

  Example     : my $annotation = CracTools::GFF::Annotation->new($gff_line);
  Description : Create a new CracTools::GFF::Annotation object
                If a gff line is passed in argument, the line will be parsed
                and loaded.
  ReturnType  : CracTools::GFF::Query
  Exceptions  : none

foundGene

  Arg [1] : String - chr
  Arg [2] : String - pos_start
  Arg [3] : String - pos_end
  Arg [4] : String - strand

  Description : Return true if there is an exon of a gene is this interval
  ReturnType  : Boolean
  Exceptions  : none

foundSameGene

  Arg [1] : String - chr
  Arg [2] : String - pos_start1
  Arg [3] : String - pos_end1
  Arg [4] : String - pos_start2
  Arg [5] : String - pos_end1
  Arg [6] : String - strand

  Description : Return true if a gene is the same gene is found is the two intervals.
  ReturnType  : Boolean
  Exceptions  : none

getBestAnnotationCandidate

  Arg [1] : String - chr
  Arg [2] : String - pos_start
  Arg [3] : String - pos_end
  Arg [4] : String - strand
  Arg [5] : (Optional) Subroutine - see C<getCandidatePriorityDefault> for more details
  Arg [6] : (Optional) Subroutine - see C<compareTwoCandidatesDefault> for more details

  Description : Return best annotation candidate according to the priorities given
                by the subroutine in argument.
  ReturnType  : Hash( feature_name => CracTools::GFF::Annotation, ...), Int(priority), String(type)

getAnnotationCandidates

  Arg [1] : String - chr
  Arg [2] : String - pos_start
  Arg [3] : String - pos_end
  Arg [4] : String - strand

  Description : Return an array with all annotation candidates overlapping the
                chromosomic region.
  ReturnType  : Array of Hash( feature_name => CracTools::GFF::Annotation, ...)

getAnnotationNearestDownCandidates

  Arg [1] : String - chr
  Arg [2] : String - pos_start
  Arg [3] : String - strand

  Description : Return an array with all annotation candidates nearest down the
                query region (without overlap).
  ReturnType  : Array of Hash( feature_name => CracTools::GFF::Annotation, ...)

getAnnotationNearestUpCandidates

  Arg [1] : String - chr
  Arg [2] : String - pos_end
  Arg [3] : String - strand

  Description : Return an array with all annotation candidates nearest up the
                query region (without overlap).
  ReturnType  : ArrayRef of HashRef{ feature_name => CracTools::GFF::Annotation, ...}

getCandidatePriorityDefault

  Arg [1] : String - pos_start
  Arg [2] : String - pos_end
  Arg [3] : hash - candidate

  Description : Default method used to give a priority to a candidate.
                You can create your own priority method to fit your specific need
                for selecting the best annotation.
                The best priority is 0. A priority of -1 means that this candidate
                should be avoided.
  ReturnType  : Array ($priority,$type) where $priority is an integer and $type a string

compareTwoCandidatesDefault

  Arg [1] : hash - candidate1
  Arg [2] : hash - candidate2
  Arg [3] : pos_start

  Description : Default method used to chose the best candidat when priority are equals
                You can create your own priority method to fit your specific need
                for selecting the best candidat.
  ReturnType  : hash - best candidat

PRIVATE METHODS

_init

  Description : init method, load GFF annotation into a
                CracTools::GFF::Query object.

_constructCandidate

  Arg [1] : String - annot_id
  Arg [2] : Hash ref - candidate
            Since this method is recursive, this is the object that
            we are constructing
  Arg [3] : Hash ref - annot_hash
            annot_hash is a hash reference where keys are annotion IDs
            and values are CracTools::GFF::Annotation objects.

  Description : _constructCandidate is a recursive method that build a
                candidate hash.
  ReturnType  : Candidate Hash ref where keys are GFF features and
                values are CracTools::GFF::Annotation objects :
                { feature => CracTools::GFF::Annotation, ...}

_constructCandidatesFromAnnotation

  Arg [1] : Hash ref - annotations
            Annotions is a hash reference where keys are coordinates
            given by CracTools::Interval::Query objects.
  Description : _constructCandidate is a recursive method that build a
                candidate hash.
  ReturnType  : Candidate array ref of all candidates built by _constructCandidate

AUTHORS

• Nicolas PHILIPPE <nicolas.philippe@inserm.fr>

• Jérôme AUDOUX <jaudoux@cpan.org>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2014 by IRB/INSERM (Institut de Recherche en Biothérapie / Institut National de la Santé et de la Recherche Médicale).

This is free software, licensed under:

  CeCILL FREE SOFTWARE LICENSE AGREEMENT, Version 2.1 dated 2013-06-21

cpanm CracTools

perl -MCPAN -e shell
install CracTools