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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::DBSQL::SliceAdaptor - A database aware adaptor responsible for the creation of Slice objects.
SYNOPSIS
use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
$slice_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
# get a slice on the entire chromosome X
$chr_slice = $slice_adaptor->fetch_by_region( 'chromosome', 'X' );
# get a slice for each clone in the database
foreach $cln_slice ( @{ $slice_adaptor->fetch_all('clone') } ) {
# do something with clone
}
# get a slice which is part of NT_004321
$spctg_slice =
$slice_adaptor->fetch_by_region( 'supercontig', 'NT_004321',
200_000, 600_000 );
# get all non-redundant slices from the highest possible coordinate
# systems
$slices = $slice_adaptor->fetch_all('toplevel');
# include non-reference regions
$slices = $slice_adaptor->fetch_all( 'toplevel', undef, 1 );
# include duplicate regions
$slices = $slice_adaptor->fetch_all( 'toplevel', undef, 0, 1 );
# split up a list of slices into smaller slices
$overlap = 1000;
$max_length = 1e6;
$slices = split_Slices( $slices, $max_length, $overlap );
# store a list of slice names in a file
open( FILE, ">$filename" ) or die("Could not open file $filename");
foreach my $slice (@$slices) {
print FILE $slice->name(), "\n";
}
close FILE;
# retrieve a list of slices from a file
open( FILE, $filename ) or die("Could not open file $filename");
while ( $name = <FILE> ) {
chomp($name);
$slice = $slice_adaptor->fetch_by_name($name);
# do something with slice
}DESCRIPTION
This module is responsible for fetching Slices representing genomic regions from a database. A Details on how slices can be used are in the Bio::EnsEMBL::Slice module.
METHODS
fetch_by_region
Arg [1] : string $coord_system_name (optional)
The name of the coordinate system of the slice to be created
This may be a name of an actual coordinate system or an alias
to a coordinate system. Valid aliases are 'seqlevel' or
'toplevel'.
Arg [2] : string $seq_region_name
The name of the sequence region that the slice will be
created on.
Arg [3] : int $start (optional, default = 1)
The start of the slice on the sequence region
Arg [4] : int $end (optional, default = seq_region length)
The end of the slice on the sequence region
Arg [5] : int $strand (optional, default = 1)
The orientation of the slice on the sequence region
Arg [6] : string $version (optional, default = default version)
The version of the coordinate system to use (e.g. NCBI33)
Arg [7] : boolean $no_fuzz (optional, default = undef (false))
If true (non-zero), do not use "fuzzy matching" (see below).
Example : $slice = $slice_adaptor->fetch_by_region('chromosome', 'X');
$slice = $slice_adaptor->fetch_by_region('clone', 'AC008066.4');
Description: Retrieves a slice on the requested region. At a minimum the
name the name of the seq_region to fetch must be provided.
If no coordinate system name is provided than a slice on the
highest ranked coordinate system with a matching
seq_region_name will be returned. If a version but no
coordinate system name is provided, the same behaviour will
apply, but only coordinate systems of the appropriate version
are considered. The same applies if the 'toplevel' coordinate
system is specified, however in this case the version is
ignored. The coordinate system should always be specified if
it is known, since this is unambiguous and faster.
Some fuzzy matching is performed if no exact match for
the provided name is found. This allows clones to be
fetched even when their version is not known. For
example fetch_by_region('clone', 'AC008066') will
retrieve the sequence_region with name 'AC008066.4'.
The fuzzy matching can be turned off by setting the
$no_fuzz argument to a true value.
If the requested seq_region is not found in the database undef
is returned.
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : throw if no seq_region_name is provided
throw if invalid coord_system_name is provided
throw if start > end is provided
Caller : general
Status : Stablefetch_by_toplevel_location
Arg [1] : string $location
Ensembl formatted location. Can be a format like
C<name:start-end>, C<name:start..end>, C<name:start:end>,
C<name:start>, C<name>. We can also support strand
specification as a +/- or 1/-1.
Location names must be separated by a C<:>. All others can be
separated by C<..>, C<:> or C<->.
Arg[2] : boolean $no_warnings
Suppress warnings from this method
Arg[3] : boolean $no_fuzz
Stop fuzzy matching of sequence regions from occuring
Arg[4] : boolean $ucsc
If we are unsuccessful at retriving a location retry taking any
possible chr prefix into account e.g. chrX and X are treated as
equivalents
Example : my $slice = $sa->fetch_by_toplevel_location('X:1-10000')
my $slice = $sa->fetch_by_toplevel_location('X:1-10000:-1')
Description : Converts an Ensembl location/region into the sequence region
name, start and end and passes them onto C<fetch_by_region()>.
The code assumes that the required slice is on the top level
coordinate system. The code assumes that location formatting
is not perfect and will perform basic cleanup before parsing.
Returntype : Bio::EnsEMBL::Slice
Exceptions : If $location is false otherwise see C<fetch_by_location()>
or C<fetch_by_region()>
Caller : General
Status : Betafetch_by_location
Arg [1] : string $location
Ensembl formatted location. Can be a format like
C<name:start-end>, C<name:start..end>, C<name:start:end>,
C<name:start>, C<name>. We can also support strand
specification as a +/- or 1/-1.
Location names must be separated by a C<:>. All others can be
separated by C<..>, C<:>, C<_> or C<->.
Arg[2] : String $coord_system_name
The coordinate system to retrieve
Arg[3] : String $coord_system_version
Optional parameter. Version of the coordinate system to fetch
Arg[4] : boolean $no_warnings
Suppress warnings from this method
Arg[5] : boolean $no_fuzz
Stop fuzzy matching of sequence regions from occuring
Arg[6] : boolean $ucsc
If we are unsuccessful at retriving a location retry taking any
possible chr prefix into account e.g. chrX and X are treated as
equivalents
Example : my $slice = $sa->fetch_by_location('X:1-10000','chromosome')
my $slice = $sa->fetch_by_location('X:1-10000:-1','toplevel')
Description : Converts an Ensembl location/region into the sequence region
name, start and end and passes them onto C<fetch_by_region()>.
The code assumes that location formatting is not perfect and
will perform basic cleanup before parsing.
Returntype : Bio::EnsEMBL::Slice
Exceptions : If $location or coordinate system is false otherwise
see C<fetch_by_region()>
Caller : General
Status : Betaparse_location_to_values
Arg [1] : string $location
Ensembl formatted location. Can be a format like
C<name:start-end>, C<name:start..end>, C<name:start:end>,
C<name:start>, C<name>. We can also support strand
specification as a +/- or 1/-1.
Location names must be separated by a C<:>. All others can be
separated by C<..>, C<:> C<_>, or C<->.
If the start is negative, start will be reset to 1 (e.g.: 1: -10-1,000')
If both start and end are negative, returns undef (e.g.: 1: -10--1,000')
Arg[2] : boolean $no_warnings
Suppress warnings from this method
Arg[3] : boolean $no_errors
Supress errors being thrown from this method
Example : my ($name, $start, $end, $strand) = $sa->parse_location_to_values('X:1..100:1);
Description : Takes in an Ensembl location String and returns the parsed
values
Returntype : List. Contains name, start, end and strand fetch_by_region_unique
Arg [1] : string $coord_system_name (optional)
The name of the coordinate system of the slice to be created
This may be a name of an actual coordinate system or an alias
to a coordinate system. Valid aliases are 'seqlevel' or
'toplevel'.
Arg [2] : string $seq_region_name
The name of the sequence region that the slice will be
created on.
Arg [3] : int $start (optional, default = 1)
The start of the slice on the sequence region
Arg [4] : int $end (optional, default = seq_region length)
The end of the slice on the sequence region
Arg [5] : int $strand (optional, default = 1)
The orientation of the slice on the sequence region
Arg [6] : string $version (optional, default = default version)
The version of the coordinate system to use (e.g. NCBI33)
Arg [7] : boolean $no_fuzz (optional, default = undef (false))
If true (non-zero), do not use "fuzzy matching" (see below).
Example : $slice = $slice_adaptor->fetch_by_region_unique('chromosome', 'HSCHR6_MHC_COX');
Description: Retrieves a slice on the requested region but returns only the unique
parts of the slice. At a minimum the
name the name of the seq_region to fetch must be provided.
If no coordinate system name is provided than a slice on the
highest ranked coordinate system with a matching
seq_region_name will be returned. If a version but no
coordinate system name is provided, the same behaviour will
apply, but only coordinate systems of the appropriate version
are considered. The same applies if the 'toplevel' coordinate
system is specified, however in this case the version is
ignored. The coordinate system should always be specified if
it is known, since this is unambiguous and faster.
Some fuzzy matching is performed if no exact match for
the provided name is found. This allows clones to be
fetched even when their version is not known. For
example fetch_by_region('clone', 'AC008066') will
retrieve the sequence_region with name 'AC008066.4'.
The fuzzy matching can be turned off by setting the
$no_fuzz argument to a true value.
If the requested seq_region is not found in the database undef
is returned.
Returntype : listref Bio::EnsEMBL::Slice
Exceptions : throw if no seq_region_name is provided
throw if invalid coord_system_name is provided
throw if start > end is provided
Caller : general
Status : Stablefetch_by_name
Arg [1] : string $name
Example : $name = 'chromosome:NCBI34:X:1000000:2000000:1';
$slice = $slice_adaptor->fetch_by_name($name);
$slice2 = $slice_adaptor->fetch_by_name($slice3->name());
Description: Fetches a slice using a slice name (i.e. the value returned by
the Slice::name method). This is useful if you wish to
store a unique identifier for a slice in a file or database or
pass a slice over a network.
Slice::name allows you to serialise/marshall a slice and this
method allows you to deserialise/unmarshal it.
Returns undef if no seq_region with the provided name exists in
the database.
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : throw if incorrent arg provided
Caller : Pipeline
Status : Stablefetch_by_seq_region_id
Arg [1] : string $seq_region_id
The internal identifier of the seq_region to create this slice
on
Arg [2] : optional start
Arg [3] : optional end
Arg [4] : optional strand
Example : $slice = $slice_adaptor->fetch_by_seq_region_id(34413);
Description: Creates a slice object of an entire seq_region using the
seq_region internal identifier to resolve the seq_region.
Returns undef if no such slice exists.
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : none
Caller : general
Status : Stableget_seq_region_id
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to fetch a seq_region_id for
Example : $srid = $slice_adaptor->get_seq_region_id($slice);
Description: Retrieves the seq_region id (in this database) given a slice
Seq region ids are not stored on the slices themselves
because they are intended to be somewhat database independant
and seq_region_ids vary accross databases.
Returntype : int
Exceptions : throw if the seq_region of the slice is not in the db
throw if incorrect arg provided
Caller : BaseFeatureAdaptor
Status : Stablefetch_all
Arg [1] : string $coord_system_name
The name of the coordinate system to retrieve slices of.
This may be a name of an acutal coordinate system or an alias
to a coordinate system. Valid aliases are 'seqlevel' or
'toplevel'.
Arg [2] : string $coord_system_version (optional)
The version of the coordinate system to retrieve slices of
Arg [3] : bool $include_non_reference (optional)
If this argument is not provided then only reference slices
will be returned. If set, both reference and non reference
slices will be returned.
Arg [4] : int $include_duplicates (optional)
If set duplicate regions will be returned.
NOTE: if you do not use this option and you have a PAR
(pseudo-autosomal region) at the beginning of your seq_region
then your slice will not start at position 1, so coordinates
retrieved from this slice might not be what you expected.
Arg[5] : bool $include_lrg (optional) (default 0)
If set lrg regions will be returned aswell.
Example : @chromos = @{$slice_adaptor->fetch_all('chromosome','NCBI33')};
@contigs = @{$slice_adaptor->fetch_all('contig')};
# get even non-reference regions
@slices = @{$slice_adaptor->fetch_all('toplevel',undef,1)};
# include duplicate regions (such as pseudo autosomal regions)
@slices = @{$slice_adaptor->fetch_all('toplevel', undef,0,1)};
Description: Retrieves slices of all seq_regions for a given coordinate
system. This is analagous to the methods fetch_all which were
formerly on the ChromosomeAdaptor, RawContigAdaptor and
CloneAdaptor classes. Slices fetched span the entire
seq_regions and are on the forward strand.
If the coordinate system with the provided name and version
does not exist an empty list is returned.
If the coordinate system name provided is 'toplevel', all
non-redundant toplevel slices are returned (note that any
coord_system_version argument is ignored in that case).
Retrieved slices can be broken into smaller slices using the
Bio::EnsEMBL::Utils::Slice module.
Returntype : listref of Bio::EnsEMBL::Slices
Exceptions : none
Caller : general
Status : Stablefetch_all_by_genome_component
Arg [1] : string $genome_component_name
The name of the genome component to retrieve slices of.
Example : @slices = @{$slice_adaptor->fetch_all_by_genome_component('A')};
Description: Returns the list of all top level slices for a a given
genome component
Returntype : listref of Bio::EnsEMBL::Slices
Exceptions : If argument is not provided or is not a valid genome
component
Caller : general
Status : Stableget_genome_component_for_slice
Arg [1] : An object of type Bio::EnsEMBL::Slice
Example : my $component = $slice->get_genome_component();
Description: Returns the genome component of a slice
Returntype : Scalar; the identifier of the genome component of the slice
Exceptions : none
Caller : general
Status : Stablefetch_all_karyotype
Example : my $top = $slice_adptor->fetch_all_karyotype()
Description: returns the list of all slices which are part of the karyotype
Returntype : listref of Bio::EnsEMBL::Slices
Caller : general
Status : At Riskis_toplevel Arg : int seq_region_id Example : my $top = $slice_adptor->is_toplevel($seq_region_id) Description: Returns 1 if slice is a toplevel slice else 0 Returntype : int Caller : Slice method is_toplevel Status : At Risk
has_karyotype Arg : int seq_region_id Example : my $karyotype = $slice_adptor->has_karyotype($seq_region_id) Description: Returns 1 if slice is a part of a karyotype else 0 Returntype : int Caller : Slice method has_karyotype Status : At Risk
get_karyotype_rank Arg : int seq_region_id Example : my $rank = $slice_adptor->get_karyotype_rank($seq_region_id) Description: Returns the rank of a slice if it is part of the karyotype else 0 Returntype : int Caller : Slice method get_karyotype_rank Status : At Risk
is_reference Arg : int seq_region_id Example : my $reference = $slice_adptor->is_reference($seq_region_id) Description: Returns 1 if slice is a reference slice else 0 Returntype : int Caller : Slice method is_reference Status : At Risk
is_circular
Arg[1] : int seq_region_id
Example : my $circular = $slice_adptor->is_circular($seq_region_id);
Description : Indicates if the sequence region was circular or not
Returntype : Booleanfetch_by_chr_band
Title : fetch_by_chr_band
Usage :
Function: create a Slice representing a series of bands
Example :
Returns : Bio::EnsEMBL::Slice
Args : the band name
Status : Stablefetch_by_exon_stable_id
Arg [1] : string $exonid
The stable id of the exon around which the slice is
desired
Arg [2] : (optional) int $size
The length of the flanking regions the slice should encompass
on either side of the exon (0 by default)
Example : $slc = $sa->fetch_by_exon_stable_id('ENSE00000302930',10);
Description: Creates a slice around the region of the specified exon.
If a context size is given, the slice is extended by that
number of basepairs on either side of the exon.
The slice will be created in the exon's native coordinate system
and in the forward orientation.
Returntype : Bio::EnsEMBL::Slice
Exceptions : Thrown if the exon is not in the database.
Caller : general
Status : Stablefetch_by_transcript_stable_id
Arg [1] : string $transcriptid
The stable id of the transcript around which the slice is
desired
Arg [2] : (optional) int $size
The length of the flanking regions the slice should encompass
on either side of the transcript (0 by default)
Example : $slc = $sa->fetch_by_transcript_stable_id('ENST00000302930',10);
Description: Creates a slice around the region of the specified transcript.
If a context size is given, the slice is extended by that
number of basepairs on either side of the
transcript.
The slice will be created in the transcript's native coordinate
system and in the forward orientation.
Returntype : Bio::EnsEMBL::Slice
Exceptions : Thrown if the transcript is not in the database.
Caller : general
Status : Stablefetch_by_transcript_id
Arg [1] : int $transcriptid
The unique database identifier of the transcript around which
the slice is desired
Arg [2] : (optional) int $size
The length of the flanking regions the slice should encompass
on either side of the transcript (0 by default)
Example : $slc = $sa->fetch_by_transcript_id(24, 1000);
Description: Creates a slice around the region of the specified transcript.
If a context size is given, the slice is extended by that
number of basepairs on either side of the
transcript.
The slice will be created in the transcript's native coordinate
system and in the forward orientation.
Returntype : Bio::EnsEMBL::Slice
Exceptions : throw on incorrect args
throw if transcript is not in database
Caller : general
Status : Stablefetch_by_gene_stable_id
Arg [1] : string $geneid
The stable id of the gene around which the slice is
desired
Arg [2] : (optional) int $size
The length of the flanking regions the slice should encompass
on either side of the gene (0 by default)
Example : $slc = $sa->fetch_by_gene_stable_id('ENSG00000012123',10);
Description: Creates a slice around the region of the specified gene.
If a context size is given, the slice is extended by that
number of basepairs on either side of the gene.
The slice will be created in the gene's native coordinate system
and in the forward orientation.
Returntype : Bio::EnsEMBL::Slice
Exceptions : throw on incorrect args
throw if transcript does not exist
Caller : general
Status : Stablefetch_by_Feature
Arg [1] : Bio::EnsEMBL::Feature $feat
The feature to fetch the slice around
Arg [2] : int size (optional)
The desired number of flanking basepairs around the feature.
The size may also be provided as a percentage of the feature
size such as 200% or 80.5%.
Example : $slice = $slice_adaptor->fetch_by_Feature($feat, 100);
Description: Retrieves a slice around a specific feature. All this really
does is return a resized version of the slice that the feature
is already on. Note that slices returned from this method
are always on the forward strand of the seq_region regardless of
the strandedness of the feature passed in.
Returntype : Bio::EnsEMBL::Slice
Exceptions : throw if the feature does not have an attached slice
throw if feature argument is not provided
Caller : fetch_by_gene_stable_id, fetch_by_transcript_stable_id,
fetch_by_gene_id, fetch_by_transcript_id
Status : Stablefetch_by_misc_feature_attribute
Arg [1] : string $attribute_type
The code of the attribute type
Arg [2] : (optional) string $attribute_value
The value of the attribute to fetch by
Arg [3] : (optional) int $size
The amount of flanking region around the misc feature desired.
Example : $slice = $sa->fetch_by_misc_feature_attribute('superctg',
'NT_030871');
$slice = $sa->fetch_by_misc_feature_attribute('synonym',
'AL00012311',
$flanking);
Description: Fetches a slice around a MiscFeature with a particular
attribute type and value. If no value is specified then
the feature with the particular attribute is used.
If no size is specified then 0 is used.
Returntype : Bio::EnsEMBL::Slice
Exceptions : Throw if no feature with the specified attribute type and value
exists in the database
Warning if multiple features with the specified attribute type
and value exist in the database.
Caller : webcode
Status : Stablefetch_by_misc_feature_set
Arg [1] : string $attribute_type
The code of the attribute type
Arg [2] : (optional) string $attribute_value
The value of the attribute to fetch by
Arg [3] : (optional) the name of the set
Arg [4] : (optional) int $size
The amount of flanking region around the misc feature desired.
Example : $slice = $sa->fetch_by_misc_feature_set('clone',
'RP11-411G9'
'tilepath');
Description: Fetches a slice around a MiscFeature with a particular
attribute type, value and set. If no value is specified then
the feature with the particular attribute is used.
A size can be specified to include flanking region
If no size is specified then 0 is used.
Returntype : Bio::EnsEMBL::Slice
Exceptions : Throw if no feature with the specified attribute type, value and set
exists in the database
Warning if multiple features with the specified attribute type, set
and value exist in the database.
Caller : webcode
Status : Stablefetch_normalized_slice_projection
Arg [1] : Bio::EnsEMBL::Slice $slice
Arg [2] : boolean $filter_projections
Optionally filter the projections to remove anything
which is the same sequence region as the given slice
Example : ( optional )
Description: gives back a project style result. The returned slices
represent the areas to which there are symlinks for the
given slice. start, end show which area on given slice is
symlinked
Returntype : [[start,end,$slice][]]
Exceptions : none
Caller : BaseFeatureAdaptor
Status : Stable_filter_Slice_projections
Arg [1] : Bio::EnsEMBL::Slice The slice the projections were made from
Arg [2] : Array The projections which were fetched from the previous slice
Description : Removes any projections which occur within the same sequence
region as the given Slice object
Returntype : ArrayRef Bio::EnsEMBL::ProjectionSegment; Returns an array
of projected segmentsstore
Arg [1] : Bio::EnsEMBL::Slice $slice
Arg [2] : (optional) $seqref reference to a string
The sequence associated with the slice to be stored.
Example : $slice = Bio::EnsEMBL::Slice->new(...);
$seq_region_id = $slice_adaptor->store($slice, \$sequence);
Description: This stores a slice as a sequence region in the database
and returns the seq region id. The passed in slice must
start at 1, and must have a valid seq_region name and coordinate
system. The attached coordinate system must already be stored in
the database. The sequence region is assumed to start at 1 and
to have a length equalling the length of the slice. The end of
the slice must equal the seq_region_length.
If the slice coordinate system is the sequence level coordinate
system then the seqref argument must also be passed. If the
slice coordinate system is NOT a sequence level coordinate
system then the sequence argument cannot be passed.
Returntype : int
Exceptions : throw if slice has no coord system.
throw if slice coord system is not already stored.
throw if slice coord system is seqlevel and no sequence is
provided.
throw if slice coord system is not seqlevel and sequence is
provided.
throw if slice does not start at 1
throw if sequence is provided and the sequence length does not
match the slice length.
throw if the SQL insert fails (e.g. on duplicate seq region)
throw if slice argument is not passed
throw if the slice end is not equal to seq_region_length
Caller : database loading scripts
Status : Stableremove
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to remove from the database
Example : $slice_adaptor->remove($slice);
Description: Removes a slice completely from the database.
All associated seq_region_attrib are removed as well.
If dna is attached to the slice, it is also removed.
Returntype : none
Exceptions : throw if slice has no coord system.
throw if slice argument is not passed
warning if slice is not stored in this database
Caller : general
Status : Stableremove_assembly
Arg [1] : Bio::EnsEMBL::Slice $asm_slice or $cmp_slice
Example : $slice_adaptor->remove_assembly( $slice );
Description: Deletes from the assembly table
where asm or cmp corresponds to slice
Do not call this method unless you really know what you are doing
Returntype : none
Exceptions : throw if slice has no coord system (cs).
throw if no slice provided, or argument is not a slice
Caller : Internal
Status : Experimentalfetch_assembly
Arg [1] : Bio::EnsEMBL::Slice $asm_slice
Arg [2] : Bio::EnsEMBL::Slice $cmp_slice
Example : $asm = $slice_adaptor->fetch_assembly( $slice1, $slice2 );
Description: Fetches from the assembly table based on the
coordinates of the two slices supplied.
Returns a mapper object mapping the two slices
Do not call this method unless you really know what you are doing
Returntype : Bio::EnsEMBL::Mapper
Exceptions : throw if either slice has no coord system (cs).
throw if there is no mapping path between coord systems
throw if there are existing mappings between either slice
and the oposite cs
Caller : Internal
Status : Experimentalstore_assembly
Arg [1] : Bio::EnsEMBL::Slice $asm_slice
Arg [2] : Bio::EnsEMBL::Slice $cmp_slice
Example : $asm = $slice_adaptor->store_assembly( $slice1, $slice2 );
Description: Creates an entry in the assembly table based on the
coordinates of the two slices supplied. Returns a string
representation of the assembly that gets created.
Returntype : string
Exceptions : throw if either slice has no coord system (cs).
throw unless the cs rank of the asm_slice is lower than the
cmp_slice.
throw if there is no mapping path between coord systems
throw if the lengths of each slice are not equal
throw if there are existing mappings between either slice
and the oposite cs
Caller : database loading scripts
Status : Experimentalprepare
Arg [1] : String $sql
Example : ( optional )
Description: overrides the default adaptor prepare method.
All slice sql will usually use the dna_db.
Returntype : DBD::sth
Exceptions : none
Caller : internal, convenience method
Status : Stablecache_toplevel_seq_mappings
Args : none
Example : $slice_adaptor->cache_toplevel_seq_mappings();
Description: caches all the assembly mappings needed for genes
Returntype : None
Exceptions : None
Caller : general
Status : At Risk
: New experimental code_create_chromosome_alias
Args : none
Example : $self->create_chromosome_alias();
Description: create chromosome alias in coordinate system with karyotype attributes
Returntype : Bio::EnsEMBL::CoordSystem, or none
Exceptions : None
Caller : general
Status : in testing