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Bio::EnsEMBL::IdMapping::SyntenyRegion Class Reference

List of all members.


Class Summary

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.
 

Definition at line 33 of file SyntenyRegion.pm.

Available Methods

public
Bio::EnsEMBL::IdMapping::SyntenyRegion 
merge ()
public A new_fast ()
public Int score ()
public Float score_location_relationship ()
public Int source_end ()
public String source_seq_region_name ()
public Int source_start ()
public Int source_strand ()
public
Bio::EnsEMBL::IdMapping::SyntenyRegion 
stretch ()
public Int target_end ()
public String target_seq_region_name ()
public Int target_start ()
public Int target_strand ()
public String to_string ()

Method Documentation

public Bio::EnsEMBL::IdMapping::SyntenyRegion Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public A Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Float Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public String Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
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public Bio::EnsEMBL::IdMapping::SyntenyRegion Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public String Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
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public String Bio::EnsEMBL::IdMapping::SyntenyRegion::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
 
Code:
click to view

The documentation for this class was generated from the following file: