|
0
|
1 =head1 LICENSE
|
|
|
2
|
|
|
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
|
|
|
4 Genome Research Limited. All rights reserved.
|
|
|
5
|
|
|
6 This software is distributed under a modified Apache license.
|
|
|
7 For license details, please see
|
|
|
8
|
|
|
9 http://www.ensembl.org/info/about/code_licence.html
|
|
|
10
|
|
|
11 =head1 CONTACT
|
|
|
12
|
|
|
13 Please email comments or questions to the public Ensembl
|
|
|
14 developers list at <dev@ensembl.org>.
|
|
|
15
|
|
|
16 Questions may also be sent to the Ensembl help desk at
|
|
|
17 <helpdesk@ensembl.org>.
|
|
|
18
|
|
|
19 =cut
|
|
|
20
|
|
|
21 =head1 NAME
|
|
|
22
|
|
|
23 Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor - adaptor/factory for MappedSlices
|
|
|
24 representing alternative assemblies
|
|
|
25
|
|
|
26 =head1 SYNOPSIS
|
|
|
27
|
|
|
28 my $slice =
|
|
|
29 $slice_adaptor->fetch_by_region( 'chromosome', 14, 900000, 950000 );
|
|
|
30
|
|
|
31 my $msc = Bio::EnsEMBL::MappedSliceContainer->new( -SLICE => $slice );
|
|
|
32
|
|
|
33 my $asa = Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
|
|
|
34
|
|
|
35 my ($mapped_slice) = @{ $asa->fetch_by_version( $msc, 'NCBIM36' ) };
|
|
|
36
|
|
|
37 =head1 DESCRIPTION
|
|
|
38
|
|
|
39 NOTE: this code is under development and not fully functional nor tested
|
|
|
40 yet. Use only for development.
|
|
|
41
|
|
|
42 This adaptor is a factory for creating MappedSlices representing
|
|
|
43 alternative assemblies and attaching them to a MappedSliceContainer. A
|
|
|
44 mapper will be created to map between the reference slice and the common
|
|
|
45 container slice coordinate system.
|
|
|
46
|
|
|
47 =head1 METHODS
|
|
|
48
|
|
|
49 new
|
|
|
50 fetch_by_version
|
|
|
51
|
|
|
52 =head1 REALTED MODULES
|
|
|
53
|
|
|
54 Bio::EnsEMBL::MappedSlice
|
|
|
55 Bio::EnsEMBL::MappedSliceContainer
|
|
|
56 Bio::EnsEMBL::Compara::AlignSlice
|
|
|
57 Bio::EnsEMBL::Compara::AlignSlice::Slice
|
|
|
58 Bio::EnsEMBL::AlignStrainSlice
|
|
|
59 Bio::EnsEMBL::StrainSlice
|
|
|
60
|
|
|
61 =cut
|
|
|
62
|
|
|
63 package Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor;
|
|
|
64
|
|
|
65 use strict;
|
|
|
66 use warnings;
|
|
|
67 no warnings 'uninitialized';
|
|
|
68
|
|
|
69 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
|
|
|
70 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
|
|
|
71 use Bio::EnsEMBL::MappedSlice;
|
|
|
72 use Bio::EnsEMBL::Mapper;
|
|
|
73 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
|
|
|
74
|
|
|
75 our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
|
|
|
76
|
|
|
77
|
|
|
78 =head2 new
|
|
|
79
|
|
|
80 Example : my $assembly_slice_adaptor =
|
|
|
81 Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
|
|
|
82 Description : Constructor.
|
|
|
83 Return type : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
|
|
|
84 Exceptions : none
|
|
|
85 Caller : general
|
|
|
86 Status : At Risk
|
|
|
87 : under development
|
|
|
88
|
|
|
89 =cut
|
|
|
90
|
|
|
91 sub new {
|
|
|
92 my $caller = shift;
|
|
|
93
|
|
|
94 my $class = ref($caller) || $caller;
|
|
|
95 my $self = $class->SUPER::new(@_);
|
|
|
96
|
|
|
97 return $self;
|
|
|
98 }
|
|
|
99
|
|
|
100
|
|
|
101 =head2 fetch_by_version
|
|
|
102
|
|
|
103 Arg[1] : Bio::EnsEMBL::MappedSliceContainer $container - the container
|
|
|
104 to attach MappedSlices to
|
|
|
105 Arg[2] : String $version - the assembly version to fetch
|
|
|
106 Example : my ($mapped_slice) = @{ $msc->fetch_by_version('NCBIM36') };
|
|
|
107 Description : Creates a MappedSlice representing an alternative assembly
|
|
|
108 version of the container's reference slice.
|
|
|
109 Return type : listref of Bio::EnsEMBL::MappedSlice
|
|
|
110 Exceptions : thrown on wrong or missing arguments
|
|
|
111 Caller : general, Bio::EnsEMBL::MappedSliceContainer
|
|
|
112 Status : At Risk
|
|
|
113 : under development
|
|
|
114
|
|
|
115 =cut
|
|
|
116
|
|
|
117 sub fetch_by_version {
|
|
|
118 my $self = shift;
|
|
|
119 my $container = shift;
|
|
|
120 my $version = shift;
|
|
|
121
|
|
|
122 # arguement check
|
|
|
123 unless ($container and ref($container) and
|
|
|
124 $container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
|
|
|
125 throw("Need a MappedSliceContainer.");
|
|
|
126 }
|
|
|
127
|
|
|
128 unless ($version) {
|
|
|
129 throw("Need an assembly version.");
|
|
|
130 }
|
|
|
131
|
|
|
132 my $slice = $container->ref_slice;
|
|
|
133
|
|
|
134 # project slice onto other assembly and construct MappedSlice for result
|
|
|
135 my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
|
|
|
136 -ADAPTOR => $self,
|
|
|
137 -CONTAINER => $container,
|
|
|
138 -NAME => $slice->name."\#mapped_$version",
|
|
|
139 );
|
|
|
140
|
|
|
141 my $cs_name = $slice->coord_system_name;
|
|
|
142
|
|
|
143 foreach my $seg (@{ $slice->project($cs_name, $version) }) {
|
|
|
144
|
|
|
145 my $proj_slice = $seg->to_Slice;
|
|
|
146
|
|
|
147 # create a Mapper to map to/from the mapped_slice artificial coord system
|
|
|
148 my $mapper = Bio::EnsEMBL::Mapper->new('mapped_slice', 'native_slice');
|
|
|
149
|
|
|
150 # tell the mapper how to map this segment
|
|
|
151 $mapper->add_map_coordinates(
|
|
|
152 'mapped_slice',
|
|
|
153 $seg->from_start,
|
|
|
154 $seg->from_end,
|
|
|
155 ($slice->strand * $proj_slice->strand),
|
|
|
156 $proj_slice->seq_region_name,
|
|
|
157 $proj_slice->start,
|
|
|
158 $proj_slice->end
|
|
|
159 );
|
|
|
160
|
|
|
161 # add the Slice/Mapper pair to the MappedSlice
|
|
|
162 $mapped_slice->add_Slice_Mapper_pair($proj_slice, $mapper);
|
|
|
163 }
|
|
|
164
|
|
|
165 return [$mapped_slice];
|
|
|
166 }
|
|
|
167
|
|
|
168
|
|
|
169 =head2 fetch_by_name
|
|
|
170
|
|
|
171 Arg[1] : Bio::EnsEMBL::MappedSliceContainer $container - the container
|
|
|
172 to attach MappedSlices to
|
|
|
173 Arg[2] : String $name - the assembly name to fetch
|
|
|
174 Arg[3] : (optional) String $version -- the version for the new assembly
|
|
|
175 Example : my ($mapped_slice) = @{ $msc->fetch_by_name('LRG1','1') };
|
|
|
176 Description : Creates a MappedSlice representing an alternative assembly
|
|
|
177 version of the container's reference slice.
|
|
|
178 Return type : listref of Bio::EnsEMBL::MappedSlice
|
|
|
179 Exceptions : thrown on wrong or missing arguments
|
|
|
180 Caller : general, Bio::EnsEMBL::MappedSliceContainer
|
|
|
181 Status : At Risk
|
|
|
182 : under development
|
|
|
183
|
|
|
184 =cut
|
|
|
185
|
|
|
186 sub fetch_by_name {
|
|
|
187 my $self = shift;
|
|
|
188 my $container = shift;
|
|
|
189 my $name = shift;
|
|
|
190 my $version = shift;
|
|
|
191
|
|
|
192 # arguement check
|
|
|
193 unless ($container and ref($container) and
|
|
|
194 $container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
|
|
|
195 throw("Need a MappedSliceContainer.");
|
|
|
196 }
|
|
|
197
|
|
|
198 unless ($name) {
|
|
|
199 throw("Need an assembly name.");
|
|
|
200 }
|
|
|
201
|
|
|
202 $version ||= '';
|
|
|
203 my $slice = $container->ref_slice;
|
|
|
204
|
|
|
205 # project slice onto other assembly and construct MappedSlice for result
|
|
|
206 my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
|
|
|
207 -ADAPTOR => $self,
|
|
|
208 -CONTAINER => $container,
|
|
|
209 -NAME => $slice->name."\#mapped_$name:$version",
|
|
|
210 );
|
|
|
211
|
|
|
212
|
|
|
213 foreach my $seg (@{ $slice->project($name, $version) }) {
|
|
|
214
|
|
|
215 my $proj_slice = $seg->to_Slice;
|
|
|
216
|
|
|
217 # create a Mapper to map to/from the mapped_slice artificial coord system
|
|
|
218 my $mapper = Bio::EnsEMBL::Mapper->new('mapped_slice', 'native_slice');
|
|
|
219
|
|
|
220 # tell the mapper how to map this segment
|
|
|
221 $mapper->add_map_coordinates(
|
|
|
222 'mapped_slice',
|
|
|
223 $seg->from_start,
|
|
|
224 $seg->from_end,
|
|
|
225 ($slice->strand * $proj_slice->strand),
|
|
|
226 $proj_slice->seq_region_name,
|
|
|
227 $proj_slice->start,
|
|
|
228 $proj_slice->end
|
|
|
229 );
|
|
|
230
|
|
|
231 # add the Slice/Mapper pair to the MappedSlice
|
|
|
232 $mapped_slice->add_Slice_Mapper_pair($proj_slice, $mapper);
|
|
|
233 }
|
|
|
234
|
|
|
235 return [$mapped_slice];
|
|
|
236 }
|
|
|
237
|
|
|
238
|
|
|
239 1;
|
|
|
240
|
