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Bio::EnsEMBL::AlignStrainSlice Class Reference

List of all members.


Class Summary

Synopsis

  $sa = $db-\>get_SliceAdaptor;

  $slice =
    $sa-\>fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );

  $strainSlice1 = $slice-\>get_by_Strain($strain_name1);
  $strainSlice2 = $slice-\>get_by_Strain($strain_name2);

  my @strainSlices;
  push @strainSlices, $strainSlice1;
  push @strainSlices, $strainSlice2;

  $alignSlice = Bio::EnsEMBL::AlignStrainSlice-\>new(
    -SLICE   =\> $slice,
    -STRAINS =\> \@strainSlices
  );

  # Get coordinates of variation in alignSlice
  my $alleleFeatures = $strainSlice1-\>get_all_AlleleFeature_Slice();

  foreach my $af ( @{$alleleFeatures} ) {
    my $new_feature = $alignSlice-\>alignFeature( $af, $strainSlice1 );
    print( "Coordinates of the feature in AlignSlice are: ",
      $new_feature-\>start, "-", $new_feature-\>end, "\n" );
  }

Description

A AlignStrainSlice object represents a region of a genome align for
certain strains.  It can be used to align certain strains to a reference
slice.
 

Definition at line 44 of file AlignStrainSlice.pm.

Available Methods

protected _get_indels ()
public Bio::EnsEMBL::Feature alignFeature ()
public Listref get_all_Slices ()
public length ()
public mapper ()
public
Bio::EnsEMBL::AlignStrainSlice 
new ()
public Bio::EnsEMBL::Slice Slice ()
public Listref strains ()

Method Documentation

protected Bio::EnsEMBL::AlignStrainSlice::_get_indels ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Feature Bio::EnsEMBL::AlignStrainSlice::alignFeature ( )
    Arg[1]      : Bio::EnsEMBL::Feature $feature
    Arg[2]      : Bio::EnsEMBL::StrainSlice $strainSlice
    Example     : $new_feature = $alignSlice->alignFeature($feature, $strainSlice);
    Description : Creates a new Bio::EnsEMBL::Feature object that aligned to 
                  the AlignStrainSlice object.
    ReturnType  : Bio::EnsEMBL::Feature
    Exceptions  : none
    Caller      : general
 
Code:
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public Listref Bio::EnsEMBL::AlignStrainSlice::get_all_Slices ( )
  Args       : none
  Description: This Slice is made of several Bio::EnsEMBL::StrainSlices
               sequence. This method returns these StrainSlices (or part of
               them) with the original coordinates 
  Returntype : listref of Bio::EnsEMBL::StrainSlice objects
  Exceptions : end should be at least as big as start
  Caller     : general
 
Code:
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public Bio::EnsEMBL::AlignStrainSlice::length ( )

Undocumented method

Code:
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public Bio::EnsEMBL::AlignStrainSlice::mapper ( )

Undocumented method

Code:
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public Bio::EnsEMBL::AlignStrainSlice Bio::EnsEMBL::AlignStrainSlice::new ( )
    Arg[1]      : Bio::EnsEMBL::Slice $Slice
    Arg[2]      : listref of Bio::EnsEMBL::StrainSlice $strainSlice
    Example     : push @strainSlices, $strainSlice1;
                  push @strainSlices, $strainSlice2;
                  .....
                  push @strainSlices, $strainSliceN;
                  $alignStrainSlice = Bio::EnsEMBL::AlignStrainSlice->new(-SLICE => $slice,
									  -STRAIN => \@strainSlices);
    Description : Creates a new Bio::EnsEMBL::AlignStrainSlice object that will contain a mapper between
                  the Slice object, plus all the indels from the different Strains
    ReturnType  : Bio::EnsEMBL::AlignStrainSlice
    Exceptions  : none
    Caller      : general
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::AlignStrainSlice::Slice ( )
  Args       : None
  Description: Returns slice where the AlignStrainSlice
               is defined
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : none
  Caller     : general
 
Code:
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public Listref Bio::EnsEMBL::AlignStrainSlice::strains ( )
  Args       : None
  Description: Returns list with all strains used to
               define this AlignStrainSlice object
  Returntype : listref of Bio::EnsEMBL::StrainSlice objects
  Exceptions : none
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: