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Bio-EnsEMBL-112.0_55
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/ Bio::EnsEMBL::IdMapping::SyntenyRegion

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::IdMapping::SyntenyRegion - object representing syntenic regions

SYNOPSIS

  # create a new SyntenyRegion from a source and a target gene
  my $sr = Bio::EnsEMBL::IdMapping::SyntenyRegion->new_fast( [
      $source_gene->start,  $source_gene->end,
      $source_gene->strand, $source_gene->seq_region_name,
      $target_gene->start,  $target_gene->end,
      $target_gene->strand, $target_gene->seq_region_name,
      $entry->score,
  ] );

  # merge with another SyntenyRegion
  my $merged_sr = $sr->merge($sr1);

  # score a gene pair against this SyntenyRegion
  my $score =
    $sr->score_location_relationship( $source_gene1, $target_gene1 );

DESCRIPTION

This object represents a synteny between a source and a target location. SyntenyRegions are built from mapped genes, and the their score is defined as the score of the gene mapping. For merged SyntenyRegions, scores are combined.

METHODS

  new_fast
  source_start
  source_end
  source_strand
  source_seq_region_name
  target_start
  target_end
  target_strand
  target_seq_region_name
  score
  merge
  stretch
  score_location_relationship
  to_string

new_fast

  Arg[1]      : Arrayref $array_ref - the arrayref to bless into the
                SyntenyRegion object 
  Example     : my $sr = Bio::EnsEMBL::IdMapping::SyntenyRegion->new_fast([
                  ]);
  Description : Constructor. On instantiation, source and target regions are
                reverse complemented so that source is always on forward strand.
  Return type : a Bio::EnsEMBL::IdMapping::SyntenyRegion object
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

source_start

  Arg[1]      : (optional) Int - source location start coordinate
  Description : Getter/setter for source location start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

source_end

  Arg[1]      : (optional) Int - source location end coordinate
  Description : Getter/setter for source location end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

source_strand

  Arg[1]      : (optional) Int - source location strand
  Description : Getter/setter for source location strand.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

source_seq_region_name

  Arg[1]      : (optional) String - source location seq_region name
  Description : Getter/setter for source location seq_region name.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

target_start

  Arg[1]      : (optional) Int - target location start coordinate
  Description : Getter/setter for target location start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

target_end

  Arg[1]      : (optional) Int - target location end coordinate
  Description : Getter/setter for target location end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

target_strand

  Arg[1]      : (optional) Int - target location strand
  Description : Getter/setter for target location strand.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

target_seq_region_name

  Arg[1]      : (optional) String - target location seq_region name
  Description : Getter/setter for target location seq_region name.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

score

  Arg[1]      : (optional) Float - score
  Description : Getter/setter for the score between source and target location.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

merge

  Arg[1]      : Bio::EnsEMBL::IdMapping::SyntenyRegion $sr - another
                SyntenyRegion
  Example     : $merged_sr = $sr->merge($other_sr);
  Description : Merges two overlapping SyntenyRegions if they meet certain
                criteria (see documentation in the code for details). Score is
                calculated as a combined distance score. If the two
                SyntenyRegions aren't mergeable, this method returns undef.
  Return type : Bio::EnsEMBL::IdMapping::SyntenyRegion or undef
  Exceptions  : warns on bad scores
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

stretch

  Arg[1]      : Float $factor - stretching factor
  Example     : $stretched_sr = $sr->stretch(2);
  Description : Extends this SyntenyRegion to span a $factor * $score more area.
  Return type : Bio::EnsEMBL::IdMapping::SyntenyRegion
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

score_location_relationship

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyGene $source_gene - source gene
  Arg[2]      : Bio::EnsEMBL::IdMapping::TinyGene $target_gene - target gene
  Example     : my $score = $sr->score_location_relationship($source_gene,
                  $target_gene);
  Description : This function calculates how well the given source location
                interpolates on given target location inside this SyntenyRegion.

                Scoring is done the following way: Source and target location
                are normalized with respect to this Regions source and target.
                Source range will then be somewhere close to 0.0-1.0 and target
                range anything around that.

                The extend of the covered area between source and target range
                is a measurement of how well they agree (smaller extend is
                better). The extend (actually 2*extend) is reduced by the size
                of the regions. This will result in 0.0 if they overlap
                perfectly and bigger values if they dont.

                This is substracted from 1.0 to give the score. The score is
                likely to be below zero, but is cut off at 0.0f.

                Finally, the score is multiplied with the score of the synteny
                itself.
  Return type : Float
  Exceptions  : warns if score out of range
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development

to_string

  Example     : print LOG $sr->to_string, "\n";
  Description : Returns a string representation of the SyntenyRegion object.
                Useful for debugging and logging.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::SyntenyFramework
  Status      : At Risk
              : under development