From 247da00f60373f1f3cd947e85842bdb667465a12 Mon Sep 17 00:00:00 2001
From: at7 <anja@ebi.ac.uk>
Date: Fri, 31 Aug 2018 13:34:31 +0100
Subject: [PATCH] deleted for release/95
---
modules/Bio/EnsEMBL/AlignStrainSlice.pm | 365 ------------------------
1 file changed, 365 deletions(-)
delete mode 100644 modules/Bio/EnsEMBL/AlignStrainSlice.pm
diff --git a/modules/Bio/EnsEMBL/AlignStrainSlice.pm b/modules/Bio/EnsEMBL/AlignStrainSlice.pm
deleted file mode 100644
index e3ace948a9..0000000000
--- a/modules/Bio/EnsEMBL/AlignStrainSlice.pm
+++ /dev/null
@@ -1,365 +0,0 @@
-=head1 LICENSE
-
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2018] 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.
-
-=cut
-
-
-=head1 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>.
-
-=cut
-
-=head1 NAME
-
-Bio::EnsEMBL::AlignStrainSlice - Represents the slice of the genome aligned with certain strains (applying the variations/indels)
-
-=head1 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" );
- }
-
-=head1 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.
-
-=head1 METHODS
-
-=cut
-
-package Bio::EnsEMBL::AlignStrainSlice;
-use strict;
-
-use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Mapper;
-use Bio::EnsEMBL::Mapper::RangeRegistry;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
-
-=head2 new
-
- Arg[1] : Bio::EnsEMBL::Slice $Slice
- Arg[2] : listref of Bio::EnsEMBL::Variation::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
-
-=cut
-
-sub new{
- my $caller = shift;
- deprecate("new is deprecated and will be removed in e95.");
- my $class = ref($caller) || $caller;
-
- my ($slice, $strainSlices) = rearrange([qw(SLICE STRAINS)],@_);
-
- #check that both StrainSlice and Slice are identical (must have been defined in the same slice)
- foreach my $strainSlice (@{$strainSlices}){
- if (($strainSlice->start != $slice->start) || ($strainSlice->end != $slice->end) || ($strainSlice->seq_region_name ne $slice->seq_region_name)){
- warning("Not possible to create Align object from different Slices");
- return [];
- }
- }
-
- return bless{'slice' => $slice,
- 'strains' => $strainSlices}, $class;
-}
-
-=head2 alignFeature
-
- Arg[1] : Bio::EnsEMBL::Feature $feature
- Arg[2] : Bio::EnsEMBL::Variation::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
-
-=cut
-
-sub alignFeature{
- my $self = shift;
- my $feature = shift;
- deprecate("alignFeature is deprecated and will be removed in e95.");
-
- #check that the object is a Feature
- if (!ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')){
- throw("Bio::EnsEMBL::Feature object expected");
- }
- #and align it to the AlignStrainSlice object
- my $mapper_strain = $self->mapper();
-
- my @results;
-
- if ($feature->start > $feature->end){
- #this is an Indel, map it with the special method
- @results = $mapper_strain->map_indel('Slice',$feature->start, $feature->end, $feature->strand,'Slice');
- #and modify the coordinates according to the length of the indel
- $results[0]->end($results[0]->start + $feature->length_diff -1);
- }
- else{
- @results = $mapper_strain->map_coordinates('Slice',$feature->start, $feature->end, $feature->strand,'Slice');
- }
- #get need start and end of the new feature, aligned ot AlignStrainSlice
- my @results_ordered = sort {$a->start <=> $b->start} @results;
-
- my %new_feature = %$feature; #make a shallow copy of the Feature
- $new_feature{'start'}= $results_ordered[0]->start();
- $new_feature{'end'} = $results_ordered[-1]->end(); #get last element of the array, the end of the slice
-
- return bless \%new_feature, ref($feature);
-
-}
-
-
-#getter for the mapper between the Slice and the different StrainSlice objects
-sub mapper{
- my $self = shift;
- deprecate("mapper is deprecated and will be removed in e95.");
-
- if (!defined $self->{'mapper'}){
- #get the alleleFeatures in all the strains
- if (!defined $self->{'indels'}){
- #when the list of indels is not defined, get them
- $self->{'indels'} = $self->_get_indels();
- }
- my $indels = $self->{'indels'}; #gaps in reference slice
- my $mapper = Bio::EnsEMBL::Mapper->new('Slice', 'AlignStrainSlice');
- my $start_slice = 1;
- my $end_slice;
- my $start_align = 1;
- my $end_align;
- my $length_indel = 0;
- my $length_acum_indel = 0;
- foreach my $indel (@{$indels}){
- $end_slice = $indel->[0] - 1;
- $end_align = $indel->[0] - 1 + $length_acum_indel; #we must consider length previous indels
-
- $length_indel = $indel->[1] - $indel->[0] + 1;
-
-
- $mapper->add_map_coordinates('Slice',$start_slice,$end_slice,1,'AlignStrainSlice',$start_align,$end_align);
-
- $mapper->add_indel_coordinates('Slice',$end_slice + 1,$end_slice,1,'AlignStrainSlice',$end_align + 1,$end_align + $length_indel);
- $start_slice = $end_slice + 1;
- $start_align = $indel->[1] + 1 + $length_acum_indel; #we must consider legnth previous indels
-
- $length_acum_indel += $length_indel;
- }
- if ($start_slice <= $self->length){
- $mapper->add_map_coordinates('Slice',$start_slice,$self->length,1,'AlignStrainSlice',$start_align,$start_align + $self->length - $start_slice)
- }
- $self->{'mapper'} = $mapper;
-
- }
- return $self->{'mapper'};
-}
-
-#returns the length of the AlignSlice: length of the Slice plus the gaps
-sub length{
- my $self = shift;
- deprecate("length is deprecated and will be removed in e95.");
-
- my $length;
- if (!defined $self->{'indels'}){
- #when the list of indels is not defined, get them
- $self->{'indels'} = $self->_get_indels();
- }
- $length = $self->{'slice'}->length;
- map {$length += ($_->[1] - $_->[0] + 1)} @{$self->{'indels'}};
- return $length;
-}
-
-=head2 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
-
-=cut
-
-sub strains{
- my $self = shift;
- deprecate("strains is deprecated and will be removed in e95.");
-
- return $self->{'strains'};
-}
-
-=head2 Slice
-
- Args : None
- Description: Returns slice where the AlignStrainSlice
- is defined
- Returntype : Bio::EnsEMBL::Slice object
- Exceptions : none
- Caller : general
-
-=cut
-
-sub Slice{
- my $self = shift;
- deprecate("Slice is deprecated and will be removed in e95.");
-
- return $self->{'slice'};
-}
-#method to retrieve, in order, a list with all the indels in the different strains
-sub _get_indels{
- my $self = shift;
- deprecate("_get_indels is deprecated and will be removed in e95.");
-
- #go throuh all the strains getting ONLY the indels (length_diff <> 0)
- my @indels;
- foreach my $strainSlice (@{$self->strains}){
- my $differences = $strainSlice->get_all_AlleleFeatures_Slice(); #need to check there are differences....
- foreach my $af (@{$differences}){
- #if length is 0, but is a -, it is still a gap in the strain
- if (($af->length_diff != 0) || ($af->length_diff == 0 && $af->allele_string =~ /-/)){
- push @indels, $af;
- }
- }
- }
- #need to overlap the gaps using the RangeRegistry module
- my $range_registry = Bio::EnsEMBL::Mapper::RangeRegistry->new();
- foreach my $indel (@indels){
- #in the reference and the strain there is a gap
- $range_registry->check_and_register(1,$indel->start,$indel->start) if ($indel->length_diff == 0);
- #deletion in reference slice
- $range_registry->check_and_register(1,$indel->start, $indel->end ) if ($indel->length_diff < 0);
- #insertion in reference slice
- $range_registry->check_and_register(1,$indel->start,$indel->start + $indel->length_diff - 1) if ($indel->length_diff > 0);
- }
- #and return all the gap coordinates....
- return $range_registry->get_ranges(1);
-}
-
-=head2 get_all_Slices
-
- Args : none
- Description: This Slice is made of several Bio::EnsEMBL::Variation::StrainSlices
- sequence. This method returns these StrainSlices (or part of
- them) with the original coordinates
- Returntype : listref of Bio::EnsEMBL::Variation::StrainSlice objects
- Exceptions : end should be at least as big as start
- Caller : general
-
-=cut
-
-sub get_all_Slices {
- my $self = shift;
-
- deprecate("get_all_Slices is deprecated and will be removed in e95.");
-
- my @strains;
- #add the reference strain
- my $dbVar = $self->Slice->adaptor->db->get_db_adaptor('variation');
- unless($dbVar) {
- warning("Variation database must be attached to core database to " .
- "retrieve variation information" );
- return '';
- }
- my $indAdaptor = $dbVar->get_IndividualAdaptor();
- my $ref_name = $indAdaptor->get_reference_strain_name;
- my $ref_strain = Bio::EnsEMBL::Variation::StrainSlice->new(
- -START => $self->Slice->{'start'},
- -END => $self->Slice->{'end'},
- -STRAND => $self->Slice->{'strand'},
- -ADAPTOR => $self->Slice->adaptor(),
- -SEQ => $self->Slice->{'seq'},
- -SEQ_REGION_NAME => $self->Slice->{'seq_region_name'},
- -SEQ_REGION_LENGTH => $self->Slice->{'seq_region_length'},
- -COORD_SYSTEM => $self->Slice->{'coord_system'},
- -STRAIN_NAME => $ref_name,
- );
- #this is a fake reference alisce, should not contain any alleleFeature
- undef $ref_strain->{'alleleFeatures'};
-
- push @strains, @{$self->strains};
- my $new_feature;
- my $indel;
- my $aligned_features;
- my $indels = (); #reference to a hash containing indels in the different strains
- #we need to realign all Features in the different Slices and add '-' in the reference Slice
- foreach my $strain (@{$self->strains}){
- foreach my $af (@{$strain->get_all_AlleleFeatures_Slice()}){
- $new_feature = $self->alignFeature($af); #align feature in AlignSlice coordinates
- push @{$aligned_features},$new_feature if($new_feature->seq_region_start <= $strain->end); #some features might map outside slice
- if ($af->start != $af->end){ #an indel, need to add to the reference, and realign in the strain
- #make a shallow copy of the indel - clear it first!
- $indel = undef;
- %{$indel} = %{$new_feature};
- bless $indel, ref($new_feature);
- $indel->allele_string('-');
- push @{$indels},$indel; #and include in the list of potential indels
- }
- }
- next if (!defined $aligned_features);
- undef $strain->{'alleleFeatures'}; #remove all features before adding new aligned features
- push @{$strain->{'alleleFeatures'}}, @{$aligned_features};
- undef $aligned_features;
- }
- push @strains, $ref_strain;
- #need to add indels in the different strains, if not present
- if (defined $indels){
- foreach my $strain (@strains){
- #inlcude the indels in the StrainSlice object
- push @{$strain->{'alignIndels'}},@{$indels};
- }
- }
- return \@strains;
-}
-
-1;
--
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