=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] 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 . Questions may also be sent to the Ensembl help desk at . =cut =head1 NAME Bio::EnsEMBL::Slice - Arbitary Slice of a genome =head1 SYNOPSIS $sa = $db->get_SliceAdaptor; $slice = $sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 ); # get some attributes of the slice my $seqname = $slice->seq_region_name(); my $start = $slice->start(); my $end = $slice->end(); # get the sequence from the slice my $seq = $slice->seq(); # get some features from the slice foreach $gene ( @{ $slice->get_all_Genes } ) { # do something with a gene } foreach my $feature ( @{ $slice->get_all_DnaAlignFeatures } ) { # do something with dna-dna alignments } =head1 DESCRIPTION A Slice object represents a region of a genome. It can be used to retrieve sequence or features from an area of interest. NOTE: The Slice is defined by its Strand, but normal behaviour for get_all_* methods is to return Features on both Strands. =head1 METHODS =cut package Bio::EnsEMBL::Slice; use vars qw(@ISA); use strict; use Bio::PrimarySeqI; use Bio::EnsEMBL::Utils::Argument qw(rearrange); use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning); use Bio::EnsEMBL::RepeatMaskedSlice; use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp); use Bio::EnsEMBL::ProjectionSegment; use Bio::EnsEMBL::Registry; use Bio::EnsEMBL::Utils::Iterator; use Bio::EnsEMBL::DBSQL::MergedAdaptor; use Bio::EnsEMBL::Mapper::RangeRegistry; use Bio::EnsEMBL::SeqRegionSynonym; use Scalar::Util qw(weaken isweak); # use Data::Dumper; my $registry = "Bio::EnsEMBL::Registry"; @ISA = qw(Bio::PrimarySeqI); =head2 new Arg [...] : List of named arguments Bio::EnsEMBL::CoordSystem COORD_SYSTEM string SEQ_REGION_NAME, int START, int END, int SEQ_REGION_LENGTH, (optional) string SEQ (optional) int STRAND, (optional, defaults to 1) Bio::EnsEMBL::DBSQL::SliceAdaptor ADAPTOR (optional) Example : $slice = Bio::EnsEMBL::Slice->new(-coord_system => $cs, -start => 1, -end => 10000, -strand => 1, -seq_region_name => 'X', -seq_region_length => 12e6, -adaptor => $slice_adaptor); Description: Creates a new slice object. A slice represents a region of sequence in a particular coordinate system. Slices can be used to retrieve sequence and features from an area of interest in a genome. Coordinates start at 1 and are inclusive. Negative coordinates or coordinates exceeding the length of the seq_region are permitted. Start must be less than or equal. to end regardless of the strand. Slice objects are immutable. Once instantiated their attributes (with the exception of the adaptor) may not be altered. To change the attributes a new slice must be created. Returntype : Bio::EnsEMBL::Slice Exceptions : throws if start, end, coordsystem or seq_region_name not specified or not of the correct type Caller : general, Bio::EnsEMBL::SliceAdaptor Status : Stable =cut sub new { my $caller = shift; #new can be called as a class or object method my $class = ref($caller) || $caller; my ($seq, $coord_system, $seq_region_name, $seq_region_length, $start, $end, $strand, $adaptor, $empty) = rearrange([qw(SEQ COORD_SYSTEM SEQ_REGION_NAME SEQ_REGION_LENGTH START END STRAND ADAPTOR EMPTY)], @_); if ( !defined($seq_region_name) ) { throw('SEQ_REGION_NAME argument is required'); } if ( !defined($start) ) { throw('START argument is required') } if ( !defined($end) ) { throw('END argument is required') } ## if ( $start > $end + 1 ) { ## throw('start must be less than or equal to end+1'); ## } if ( !defined($seq_region_length) ) { $seq_region_length = $end } if ( $seq_region_length <= 0 ) { throw('SEQ_REGION_LENGTH must be > 0'); } if ( defined($seq) && CORE::length($seq) != ( $end - $start + 1 ) ) { throw('SEQ must be the same length as the defined LENGTH not ' . CORE::length($seq) . ' compared to ' . ( $end - $start + 1 ) ); } if(defined($coord_system)) { if(!ref($coord_system) || !$coord_system->isa('Bio::EnsEMBL::CoordSystem')){ throw('COORD_SYSTEM argument must be a Bio::EnsEMBL::CoordSystem'); } if($coord_system->is_top_level()) { throw('Cannot create slice on toplevel CoordSystem.'); } } else { warning("Slice without coordinate system"); } $strand ||= 1; if($strand != 1 && $strand != -1) { throw('STRAND argument must be -1 or 1'); } if(defined($adaptor)) { if(!ref($adaptor) || !$adaptor->isa('Bio::EnsEMBL::DBSQL::SliceAdaptor')) { throw('ADAPTOR argument must be a Bio::EnsEMBL::DBSQL::SliceAdaptor'); } } my $self = bless {'coord_system' => $coord_system, 'seq' => $seq, 'seq_region_name' => $seq_region_name, 'seq_region_length' => $seq_region_length, 'start' => int($start), 'end' => int($end), 'strand' => $strand}, $class; $self->adaptor($adaptor); return $self; } =head2 new_fast Arg [1] : hashref to be blessed Description: Construct a new Bio::EnsEMBL::Slice using the hashref. Exceptions : none Returntype : Bio::EnsEMBL::Slice Caller : general Status : Stable =cut sub new_fast { my $class = shift; my $hashref = shift; my $self = bless $hashref, $class; weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) ); return $self; } =head2 adaptor Arg [1] : (optional) Bio::EnsEMBL::DBSQL::SliceAdaptor $adaptor Example : $adaptor = $slice->adaptor(); Description: Getter/Setter for the slice object adaptor used by this slice for database interaction. Returntype : Bio::EnsEMBL::DBSQL::SliceAdaptor Exceptions : thorws if argument passed is not a SliceAdaptor Caller : general Status : Stable =cut sub adaptor{ my $self = shift; if(@_) { my $ad = shift; if(defined($ad)) { if(!ref($ad) || !$ad->isa('Bio::EnsEMBL::DBSQL::SliceAdaptor')) { throw('Argument must be a Bio::EnsEMBL::DBSQL::SliceAdaptor'); } } weaken($self->{'adaptor'} = $ad); } return $self->{'adaptor'}; } =head2 seq_region_name Arg [1] : none Example : $seq_region = $slice->seq_region_name(); Description: Returns the name of the seq_region that this slice is on. For example if this slice is in chromosomal coordinates the seq_region_name might be 'X' or '10'. This function was formerly named chr_name, but since slices can now be on coordinate systems other than chromosomal it has been changed. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub seq_region_name { my $self = shift; return $self->{'seq_region_name'}; } =head2 seq_region_start Example : $seq_region_start = $slice->seq_region_start(); Description: Returns the start position of this slice relative to the start of the sequence region that it was created on. Since slices are always in genomic coordinates this is an alias to start() Returntype : int Exceptions : none Caller : general Status : Stable =cut sub seq_region_start { my $self = shift; return $self->start(); } =head2 seq_region_end Example : $seq_region_end = $slice->seq_region_end(); Description: Returns the end position of this slice relative to the start of the sequence region that it was created on. Since slices are always in genomic coordinates this is an alias to end() Returntype : int Exceptions : none Caller : general Status : Stable =cut sub seq_region_end { my $self = shift; return $self->end(); } =head2 seq_region_length Arg [1] : none Example : $seq_region_length = $slice->seq_region_length(); Description: Returns the length of the entire seq_region that this slice is on. For example if this slice is on a chromosome this will be the length (in basepairs) of the entire chromosome. Returntype : int Exceptions : none Caller : general Status : Stable =cut sub seq_region_length { my $self = shift; return $self->{'seq_region_length'}; } =head2 coord_system Arg [1] : none Example : print $slice->coord_system->name(); Description: Returns the coordinate system that this slice is on. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : general Status : Stable =cut sub coord_system { my $self = shift; return $self->{'coord_system'}; } =head2 source Arg [1] : (optional) String $value Example : print $slice->source(); Description: Returns the source this slice is coming from Returntype : string Exceptions : none Caller : general Status : Stable =cut sub source { my $self = shift; $self->{'source'} = shift if (@_); return $self->{'source'}; } =head2 coord_system_name Arg [1] : none Example : print $slice->coord_system_name() Description: Convenience method. Gets the name of the coord_system which this slice is on. Returns undef if this Slice does not have an attached CoordSystem. Returntype: string or undef Exceptions: none Caller : general Status : Stable =cut sub coord_system_name { my $self = shift; my $csystem = $self->{'coord_system'}; return ($csystem) ? $csystem->name() : undef; } =head2 centrepoint Arg [1] : none Example : $cp = $slice->centrepoint(); Description: Returns the mid position of this slice relative to the start of the sequence region that it was created on. Coordinates are inclusive and start at 1. Returntype : int Exceptions : none Caller : general Status : Stable =cut sub centrepoint { my $self = shift; return ($self->{'start'}+$self->{'end'})/2; } =head2 start Arg [1] : none Example : $start = $slice->start(); Description: Returns the start position of this slice relative to the start of the sequence region that it was created on. Coordinates are inclusive and start at 1. Negative coordinates or coordinates exceeding the length of the sequence region are permitted. Start is always less than or equal to end regardless of the orientation of the slice. Returntype : int Exceptions : none Caller : general Status : Stable =cut sub start { my $self = shift; return $self->{'start'}; } =head2 end Arg [1] : none Example : $end = $slice->end(); Description: Returns the end position of this slice relative to the start of the sequence region that it was created on. Coordinates are inclusive and start at 1. Negative coordinates or coordinates exceeding the length of the sequence region are permitted. End is always greater than or equal to start regardless of the orientation of the slice. Returntype : int Exceptions : none Caller : general Status : Stable =cut sub end { my $self = shift; return $self->{'end'}; } =head2 strand Arg [1] : none Example : $strand = $slice->strand(); Description: Returns the orientation of this slice on the seq_region it has been created on Returntype : int (either 1 or -1) Exceptions : none Caller : general, invert Status : Stable =cut sub strand{ my $self = shift; return $self->{'strand'}; } =head2 name Arg [1] : none Example : my $results = $cache{$slice->name()}; Description: Returns the name of this slice. The name is formatted as a colon delimited string with the following attributes: coord_system:version:seq_region_name:start:end:strand Slices with the same name are equivalent and thus the name can act as a hash key. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub name { my $self = shift; my $cs = $self->{'coord_system'}; return join(':', ($cs) ? $cs->name() : '', ($cs) ? $cs->version() : '', $self->{'seq_region_name'}, $self->{'start'}, $self->{'end'}, $self->{'strand'}); } =head2 length Arg [1] : none Example : $length = $slice->length(); Description: Returns the length of this slice in basepairs Returntype : int Exceptions : none Caller : general Status : Stable =cut sub length { my ($self) = @_; my $length = $self->{'end'} - $self->{'start'} + 1; if ( $self->{'start'} > $self->{'end'} && $self->is_circular() ) { $length += $self->{'seq_region_length'}; } return $length; } =head2 is_reference Arg : none Example : my $reference = $slice->is_reference() Description: Returns 1 if slice is a reference slice else 0 Returntype : int Caller : general Status : At Risk =cut sub is_reference { my ($self) = @_; if ( !defined( $self->{'is_reference'} ) ) { $self->{'is_reference'} = $self->adaptor()->is_reference( $self->get_seq_region_id() ); } return $self->{'is_reference'}; } =head2 is_toplevel Arg : none Example : my $top = $slice->is_toplevel() Description: Returns 1 if slice is a toplevel slice else 0 Returntype : int Caller : general Status : At Risk =cut sub is_toplevel { my ($self) = @_; if ( !defined( $self->{'toplevel'} ) ) { $self->{'toplevel'} = $self->adaptor()->is_toplevel( $self->get_seq_region_id() ); } return $self->{'toplevel'}; } =head2 has_karyotype Arg : none Example : my $top = $slice->has_karyotype() Description: Returns 1 if slice is part of the karyotype else 0 Returntype : int Caller : general Status : At Risk =cut sub has_karyotype { my ($self) = @_; if ( !defined( $self->{'karyotype'} ) ) { $self->{'karyotype'} = $self->adaptor()->has_karyotype( $self->get_seq_region_id() ); } return $self->{'karyotype'}; } =head2 karyotype_rank Arg : none Example : my $rank = $slice->karyotype_rank() Description: Returns the numeric ranking in the karyotype. Otherwise 0 is returned Returntype : int Caller : general Status : At Risk =cut sub karyotype_rank { my ($self) = @_; if(! defined( $self->{karyotype_rank})) { my $rank = $self->adaptor()->get_karyotype_rank($self->get_seq_region_id()); $self->{karyotype_rank} = $rank if $rank; } return $self->{karyotype_rank} || 0; } =head2 is_circular Arg : none Example : my $circ = $slice->is_circular() Description: Returns 1 if slice is a circular slice else 0 Returntype : int Caller : general Status : Stable =cut sub is_circular { my ($self) = @_; my $adaptor = $self->adaptor(); return 0 if ! defined $adaptor; if (! exists $self->{'circular'}) { my $id = $adaptor->get_seq_region_id($self); $self->{circular} = $adaptor->is_circular($id); } return $self->{circular}; } =head2 invert Arg [1] : none Example : $inverted_slice = $slice->invert; Description: Creates a copy of this slice on the opposite strand and returns it. Returntype : Bio::EnsEMBL::Slice Exceptions : none Caller : general Status : Stable =cut sub invert { my $self = shift; # make a shallow copy of the slice via a hash copy and flip the strand my %s = %$self; $s{'strand'} = $self->{'strand'} * -1; # reverse compliment any attached sequence reverse_comp(\$s{'seq'}) if($s{'seq'}); # bless and return the copy return bless \%s, ref $self; } =head2 seq Arg [1] : none Example : print "SEQUENCE = ", $slice->seq(); Description: Returns the sequence of the region represented by this slice formatted as a string. Only available for the default coord_system Returntype : string Exceptions : none Caller : general Status : Stable =cut sub seq { my $self = shift; # special case for in-between (insert) coordinates return '' if($self->start() == $self->end() + 1); return $self->{'seq'} if($self->{'seq'}); if($self->adaptor()) { my $seqAdaptor = $self->adaptor()->db()->get_SequenceAdaptor(); return ${$seqAdaptor->fetch_by_Slice_start_end_strand($self,1,undef,1)}; } # no attached sequence, and no db, so just return Ns return 'N' x $self->length(); } =head2 subseq Arg [1] : int $startBasePair relative to start of slice, which is 1. Arg [2] : int $endBasePair relative to start of slice. Arg [3] : (optional) int $strand The strand of the slice to obtain sequence from. Default value is 1. Description: returns string of dna sequence Returntype : txt Exceptions : end should be at least as big as start strand must be set Caller : general Status : Stable =cut sub subseq { my ( $self, $start, $end, $strand ) = @_; if ( $end+1 < $start ) { throw("End coord + 1 is less than start coord"); } # handle 'between' case for insertions return '' if( $start == $end + 1); $strand = 1 unless(defined $strand); if ( $strand != -1 && $strand != 1 ) { throw("Invalid strand [$strand] in call to Slice::subseq."); } my $subseq; if($self->adaptor){ my $seqAdaptor = $self->adaptor->db->get_SequenceAdaptor(); $subseq = ${$seqAdaptor->fetch_by_Slice_start_end_strand ( $self, $start, $end, $strand )}; } else { ## check for gap at the beginning and pad it with Ns if ($start < 1) { $subseq = "N" x (1 - $start); $start = 1; } $subseq .= substr ($self->seq(), $start-1, $end - $start + 1); ## check for gap at the end and pad it with Ns if ($end > $self->length()) { $subseq .= "N" x ($end - $self->length()); } reverse_comp(\$subseq) if($strand == -1); } return $subseq; } =head2 sub_Slice_Iterator Arg[1] : int The chunk size to request Example : my $i = $slice->sub_Slice_Iterator(60000); while($i->has_next()) { warn $i->next()->name(); } Description : Returns an iterator which batches subslices of this Slice in the requested chunk size Returntype : Bio::EnsEMBL::Utils::Iterator next() will return the next chunk of Slice Exceptions : None =cut sub sub_Slice_Iterator { my ($self, $chunk_size) = @_; throw "Need a chunk size to divide the slice by" if ! $chunk_size; my $here = 1; my $end = $self->length(); my $iterator_sub = sub { while($here <= $end) { my $there = $here + $chunk_size - 1; $there = $end if($there > $end); my $slice = $self->sub_Slice($here, $there); $here = $there + 1; return $slice; } return; }; return Bio::EnsEMBL::Utils::Iterator->new($iterator_sub); } =head2 assembly_exception_type Example : $self->assembly_exception_type(); Description : Returns the type of slice this is. If it is reference then you will get 'REF' back. Otherwise you will get the first element from C. If no assembly exception exists you will get an empty string back. Returntype : String Exceptions : None Caller : Public Status : Beta =cut sub assembly_exception_type { my ($self) = @_; my $type = q{}; if($self->is_reference()) { $type = 'REF'; } else { my $assembly_exceptions = $self->get_all_AssemblyExceptionFeatures(); if(@{$assembly_exceptions}) { $type = $assembly_exceptions->[0]->type(); } } return $type; } =head2 is_chromosome Example : print ($slice->is_chromosome()) ? 'I am a chromosome' : 'Not one'; Description : A chromosome is a slice with a karyotype rank assigned to it. Returntype : Boolean indicates if the current object is a chromosome Exceptions : None =cut sub is_chromosome { my ($self) = @_; return $self->has_karyotype(); } =head2 get_base_count Arg [1] : none Example : $c_count = $slice->get_base_count->{'c'}; Description: Retrieves a hashref containing the counts of each bases in the sequence spanned by this slice. The format of the hash is : { 'a' => num, 'c' => num, 't' => num, 'g' => num, 'n' => num, '%gc' => num } All bases which are not in the set [A,a,C,c,T,t,G,g] are included in the 'n' count. The 'n' count could therefore be inclusive of ambiguity codes such as 'y'. The %gc is the ratio of GC to AT content as in: total(GC)/total(ACTG) * 100 This function is conservative in its memory usage and scales to work for entire chromosomes. Returntype : hashref Exceptions : none Caller : general Status : Stable =cut sub get_base_count { my $self = shift; my $a = 0; my $c = 0; my $t = 0; my $g = 0; my $start = 1; my $end; my $RANGE = 100_000; my $len = $self->length(); my $seq; while ( $start <= $len ) { $end = $start + $RANGE - 1; $end = $len if ( $end > $len ); $seq = $self->subseq( $start, $end ); $a += $seq =~ tr/Aa//; $c += $seq =~ tr/Cc//; $t += $seq =~ tr/Tt//; $g += $seq =~ tr/Gg//; $start = $end + 1; } my $actg = $a + $c + $t + $g; my $gc_content = 0; if ( $actg > 0 ) { # Avoid dividing by 0 $gc_content = sprintf( "%1.2f", ( ( $g + $c )/$actg )*100 ); } return { 'a' => $a, 'c' => $c, 't' => $t, 'g' => $g, 'n' => $len - $actg, '%gc' => $gc_content }; } =head2 project Arg [1] : string $name The name of the coordinate system to project this slice onto Arg [2] : string $version The version of the coordinate system (such as 'NCBI34') to project this slice onto Example : my $clone_projection = $slice->project('clone'); foreach my $segment (@$clone_projection) { my $clone = $segment->to_Slice(); print $slice->seq_region_name(), ':', $segment->from_start(), '-', $segment->from_end(), ' -> ', $clone->seq_region_name(), ':', $clone->start(), '-',$clone->end(), ':', $clone->strand(), "\n"; } Description: Returns the results of 'projecting' this slice onto another coordinate system. Projecting to a coordinate system that the slice is assembled from is analagous to retrieving a tiling path. This method may also be used to 'project up' to a higher level coordinate system, however. This method returns a listref of triplets [start,end,slice] which represents the projection. The start and end defined the region of this slice which is made up of the third value of the triplet: a slice in the requested coordinate system. Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which can also be used as [$start,$end,$slice] triplets Exceptions : none Caller : general Status : Stable =cut sub project { my $self = shift; my $cs_name = shift; my $cs_version = shift; throw('Coord_system name argument is required') if(!$cs_name); my $slice_adaptor = $self->adaptor(); if(!$slice_adaptor) { warning("Cannot project without attached adaptor."); return []; } if(!$self->coord_system()) { warning("Cannot project without attached coord system."); return []; } my $db = $slice_adaptor->db(); my $csa = $db->get_CoordSystemAdaptor(); my $cs = $csa->fetch_by_name($cs_name, $cs_version); my $slice_cs = $self->coord_system(); if(!$cs) { throw("Cannot project to unknown coordinate system " . "[$cs_name $cs_version]"); } # no mapping is needed if the requested coord system is the one we are in # but we do need to check if some of the slice is outside of defined regions if($slice_cs->equals($cs)) { return $self->_constrain_to_region(); } my @projection; # decompose this slice into its symlinked components. # this allows us to handle haplotypes and PARs my $normal_slice_proj = $slice_adaptor->fetch_normalized_slice_projection($self); foreach my $segment (@$normal_slice_proj) { my $normal_slice = $segment->[2]; $slice_cs = $normal_slice->coord_system(); my $asma = $db->get_AssemblyMapperAdaptor(); my $asm_mapper = $asma->fetch_by_CoordSystems($slice_cs, $cs); next unless defined $asm_mapper; # perform the mapping between this slice and the requested system my @coords = $asm_mapper->map($normal_slice->seq_region_name(), $normal_slice->start(), $normal_slice->end(), $normal_slice->strand(), $slice_cs, undef, undef, 1); # construct a projection from the mapping results and return it foreach my $coord (@coords) { my $original = $coord->{original}; my $mapped = $coord->{mapped}; # skip gaps next unless $mapped->isa('Bio::EnsEMBL::Mapper::Coordinate'); my $mapped_start = $mapped->start(); my $mapped_end = $mapped->end(); my ($current_start, $current_end); if ($self->strand == 1) { $current_start = $original->start() - $self->start + 1; $current_end = $original->end() - $self->start + 1; } else { $current_start = $self->end() - $original->end + 1; $current_end = $self->end - $original->start + 1; } my $coord_cs = $mapped->coord_system(); # If the normalised projection just ended up mapping to the # same coordinate system we were already in then we should just # return the original region. This can happen for example, if we # were on a PAR region on Y which refered to X and a projection to # 'toplevel' was requested. if($coord_cs->equals($slice_cs)) { # trim off regions which are not defined return $self->_constrain_to_region(); } #create slices for the mapped-to coord system my $slice = $slice_adaptor->fetch_by_seq_region_id($mapped->id(), $mapped_start, $mapped_end, $mapped->strand()); if ($current_end > $slice->seq_region_length() && $slice->is_circular ) { $current_end -= $slice->seq_region_length(); } push @projection, bless([$current_start, $current_end, $slice], "Bio::EnsEMBL::ProjectionSegment"); } } return \@projection; } sub _constrain_to_region { my $self = shift; my $entire_len = $self->seq_region_length(); #if the slice has negative coordinates or coordinates exceeding the #exceeding length of the sequence region we want to shrink the slice to #the defined region if($self->{'start'} > $entire_len || $self->{'end'} < 1) { #none of this slice is in a defined region return []; } my $right_contract = 0; my $left_contract = 0; if($self->{'end'} > $entire_len) { $right_contract = $entire_len - $self->{'end'}; } if($self->{'start'} < 1) { $left_contract = $self->{'start'} - 1; } my $new_slice; if($left_contract || $right_contract) { #if slice in negative strand, need to swap contracts if ($self->strand == 1) { $new_slice = $self->expand($left_contract, $right_contract); } elsif ($self->strand == -1) { $new_slice = $self->expand($right_contract, $left_contract); } } else { $new_slice = $self; } return [bless [1-$left_contract, $self->length()+$right_contract, $new_slice], "Bio::EnsEMBL::ProjectionSegment" ]; } =head2 expand Arg [1] : (optional) int $five_prime_expand The number of basepairs to shift this slices five_prime coordinate by. Positive values make the slice larger, negative make the slice smaller. coordinate left. Default = 0. Arg [2] : (optional) int $three_prime_expand The number of basepairs to shift this slices three_prime coordinate by. Positive values make the slice larger, negative make the slice smaller. Default = 0. Arg [3] : (optional) bool $force_expand if set to 1, then the slice will be contracted even in the case when shifts $five_prime_expand and $three_prime_expand overlap. In that case $five_prime_expand and $three_prime_expand will be set to a maximum possible number and that will result in the slice which would have only 2pbs. Default = 0. Arg [4] : (optional) int* $fpref The reference to a number of basepairs to shift this slices five_prime coordinate by. Normally it would be set to $five_prime_expand. But in case when $five_prime_expand shift can not be applied and $force_expand is set to 1, then $$fpref will contain the maximum possible shift Arg [5] : (optional) int* $tpref The reference to a number of basepairs to shift this slices three_prime coordinate by. Normally it would be set to $three_prime_expand. But in case when $five_prime_expand shift can not be applied and $force_expand is set to 1, then $$tpref will contain the maximum possible shift Example : my $expanded_slice = $slice->expand( 1000, 1000); my $contracted_slice = $slice->expand(-1000,-1000); my $shifted_right_slice = $slice->expand(-1000, 1000); my $shifted_left_slice = $slice->expand( 1000,-1000); my $forced_contracted_slice = $slice->expand(-1000,-1000, 1, \$five_prime_shift, \$three_prime_shift); Description: Returns a slice which is a resized copy of this slice. The start and end are moved outwards from the center of the slice if positive values are provided and moved inwards if negative values are provided. This slice remains unchanged. A slice may not be contracted below 1bp but may grow to be arbitrarily large. Returntype : Bio::EnsEMBL::Slice Exceptions : warning if an attempt is made to contract the slice below 1bp Caller : general Status : Stable =cut sub expand { my $self = shift; my $five_prime_shift = shift || 0; my $three_prime_shift = shift || 0; my $force_expand = shift || 0; my $fpref = shift; my $tpref = shift; if ( $self->{'seq'} ) { warning( "Cannot expand a slice which has a manually attached sequence "); return undef; } my $sshift = $five_prime_shift; my $eshift = $three_prime_shift; if ($sshift == 0 && $eshift == 0) { return $self; } if ( $self->{'strand'} != 1 ) { $eshift = $five_prime_shift; $sshift = $three_prime_shift; } my $new_start = $self->{'start'} - $sshift; my $new_end = $self->{'end'} + $eshift; # Wrap around on circular slices if (( $new_start <= 0 || $new_start > $self->seq_region_length() || $new_end <= 0 || $new_end > $self->seq_region_length() ) && ( $self->is_circular() ) ) { if ( $new_start <= 0 ) { $new_start = $self->seq_region_length() + $new_start; } if ( $new_start > $self->seq_region_length() ) { $new_start -= $self->seq_region_length(); } if ( $new_end <= 0 ) { $new_end = $self->seq_region_length() + $new_end; } if ( $new_end > $self->seq_region_length() ) { $new_end -= $self->seq_region_length(); } } if ( $new_start > $new_end && (not $self->is_circular() ) ) { if ($force_expand) { # Apply max possible shift, if force_expand is set if ( $sshift < 0 ) { # if we are contracting the slice from the start - move the # start just before the end $new_start = $new_end - 1; $sshift = $self->{start} - $new_start; } if ( $new_start > $new_end ) { # if the slice still has a negative length - try to move the # end if ( $eshift < 0 ) { $new_end = $new_start + 1; $eshift = $new_end - $self->{end}; } } # return the values by which the primes were actually shifted $$tpref = $self->{strand} == 1 ? $eshift : $sshift; $$fpref = $self->{strand} == 1 ? $sshift : $eshift; } if ( $new_start > $new_end ) { throw('Slice start cannot be greater than slice end'); } } #fastest way to copy a slice is to do a shallow hash copy my %new_slice = %$self; $new_slice{'start'} = int($new_start); $new_slice{'end'} = int($new_end); return bless \%new_slice, ref($self); } ## end sub expand =head2 constrain_to_seq_region Example : $new_slice = $slice->expand(1000,10000); $new_slice = $new_slice->constrain_to_seq_region(); Description: Used to prevent overly zealous expand calls going off the end of the sequence region. It contracts the start and end where needed and produces a slice copy with the tweaked coordinates. Returntype : Bio::EnsEMBL::Slice =cut sub constrain_to_seq_region { my ($self) = @_; # circular calculations should already be taken care of if ($self->is_circular) {return $self} my $new_start = $self->start; my $new_end = $self->end; my $seq_region = $self->seq_region_Slice; if ($new_start < $seq_region->start) {$new_start = $seq_region->start} if ($new_end > $seq_region->end) {$new_end = $seq_region->end} my %new_slice = %$self; $new_slice{'start'} = $new_start; $new_slice{'end'} = $new_end; return bless \%new_slice, ref($self); } =head2 sub_Slice Arg 1 : int $start, refers to the start of the subslice relative to the input slice Arg 2 : int $end, refers to the end of the subslice relative to the input slice Arge [3] : int $strand Example : none Description: Makes another Slice that covers only part of this Slice If a Slice is requested which lies outside of the boundaries of this function will return undef. This means that behaviour will be consistant whether or not the slice is attached to the database (i.e. if there is attached sequence to the slice). Alternatively the expand() method or the SliceAdaptor::fetch_by_region method can be used instead. Returntype : Bio::EnsEMBL::Slice or undef if arguments are wrong Exceptions : none Caller : general Status : Stable =cut sub sub_Slice { my ( $self, $start, $end, $strand ) = @_; my $length = $self->length(); if( $start < 1 || $start > $length ) { # throw( "start argument not valid" ); return undef; } if( $end < $start || $end > $length ) { # throw( "end argument not valid" ) return undef; } my ( $new_start, $new_end, $new_strand, $new_seq ); if( ! defined $strand ) { $strand = 1; } if( $self->{'strand'} == 1 ) { $new_start = $self->{'start'} + $start - 1; $new_end = $self->{'start'} + $end - 1; $new_strand = $strand; } else { $new_start = $self->{'end'} - $end + 1;; $new_end = $self->{'end'} - $start + 1; $new_strand = -$strand; } if( defined $self->{'seq'} ) { $new_seq = $self->subseq( $start, $end, $strand ); } #fastest way to copy a slice is to do a shallow hash copy my $new_slice = {%{$self}}; $new_slice->{'start'} = int($new_start); $new_slice->{'end'} = int($new_end); $new_slice->{'strand'} = $new_strand; if( $new_seq ) { $new_slice->{'seq'} = $new_seq; } weaken($new_slice->{adaptor}); return bless $new_slice, ref($self); } =head2 seq_region_Slice Arg [1] : none Example : $slice = $slice->seq_region_Slice(); Description: Returns a slice which spans the whole seq_region which this slice is on. For example if this is a slice which spans a small region of chromosome X, this method will return a slice which covers the entire chromosome X. The returned slice will always have strand of 1 and start of 1. This method cannot be used if the sequence of the slice has been set manually. Returntype : Bio::EnsEMBL::Slice Exceptions : warning if called when sequence of Slice has been set manually. Caller : general Status : Stable =cut sub seq_region_Slice { my $self = shift; if($self->{'seq'}){ warning("Cannot get a seq_region_Slice of a slice which has manually ". "attached sequence "); return undef; } # quick shallow copy my $slice; %{$slice} = %{$self}; bless $slice, ref($self); weaken($slice->{adaptor}); $slice->{'start'} = 1; $slice->{'end'} = $slice->{'seq_region_length'}; $slice->{'strand'} = 1; return $slice; } =head2 get_seq_region_id Arg [1] : none Example : my $seq_region_id = $slice->get_seq_region_id(); Description: Gets the internal identifier of the seq_region that this slice is on. Note that this function will not work correctly if this slice does not have an attached adaptor. Also note that it may be better to go through the SliceAdaptor::get_seq_region_id method if you are working with multiple databases since is possible to work with slices from databases with different internal seq_region identifiers. Returntype : int or undef if slices does not have attached adaptor Exceptions : warning if slice is not associated with a SliceAdaptor Caller : assembly loading scripts, general Status : Stable =cut sub get_seq_region_id { my ($self) = @_; if($self->adaptor) { return $self->adaptor->get_seq_region_id($self); } else { warning('Cannot retrieve seq_region_id without attached adaptor.'); return undef; } } =head2 get_genome_component Arg [] : none Example : my $genome_component = $slice->get_genome_component(); Description: Returns the genome component of the slice Returntype : Scalar; the identifier of the genome component of the slice Exceptions : none Caller : general Status : Stable =cut sub get_genome_component { my $self = shift; return $self->adaptor->get_genome_component_for_slice($self); } =head2 get_all_Attributes Arg [1] : optional string $attrib_code The code of the attribute type to retrieve values for. Example : ($htg_phase) = @{$slice->get_all_Attributes('htg_phase')}; @slice_attributes = @{$slice->get_all_Attributes()}; Description: Gets a list of Attributes of this slice''s seq_region. Optionally just get Attrubutes for given code. Returntype : listref Bio::EnsEMBL::Attribute Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_Attributes { my ($self, $attrib_code) = @_; if(my $adaptor = $self->_get_CoreAdaptor('Attribute')) { my $attribs = $adaptor->fetch_all_by_Slice($self); if(defined $attrib_code) { my $uc_attrib = uc($attrib_code); return [ grep { uc($_->code()) eq $uc_attrib } @{$attribs}]; } return $attribs; } return []; } =head2 get_all_PredictionTranscripts Arg [1] : (optional) string $logic_name The name of the analysis used to generate the prediction transcripts obtained. Arg [2] : (optional) boolean $load_exons If set to true will force loading of all PredictionExons immediately rather than loading them on demand later. This is faster if there are a large number of PredictionTranscripts and the exons will be used. Example : @transcripts = @{$slice->get_all_PredictionTranscripts}; Description: Retrieves the list of prediction transcripts which overlap this slice with logic_name $logic_name. If logic_name is not defined then all prediction transcripts are retrieved. Returntype : listref of Bio::EnsEMBL::PredictionTranscript Exceptions : warning if slice does not have attached adaptor Caller : none Status : Stable =cut sub get_all_PredictionTranscripts { my ($self,$logic_name, $load_exons) = @_; if(!$self->adaptor()) { warning('Cannot get PredictionTranscripts without attached adaptor'); return []; } my $pta = $self->adaptor()->db()->get_PredictionTranscriptAdaptor(); return $pta->fetch_all_by_Slice($self, $logic_name, $load_exons); } =head2 get_all_DnaAlignFeatures Arg [1] : (optional) string $logic_name The name of the analysis performed on the dna align features to obtain. Arg [2] : (optional) float $score The mimimum score of the features to retrieve Arg [3] : (optional) string $dbtype The name of an attached database to retrieve the features from instead, e.g. 'otherfeatures'. Arg [4] : (optional) float hcoverage The minimum hcoverage od the featurs to retrieve Example : @dna_dna_align_feats = @{$slice->get_all_DnaAlignFeatures}; Description: Retrieves the DnaDnaAlignFeatures which overlap this slice with logic name $logic_name and with score above $score. If $logic_name is not defined features of all logic names are retrieved. If $score is not defined features of all scores are retrieved. Strand of the Slice is not considered. Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_DnaAlignFeatures { my ($self, $logic_name, $score, $dbtype, $hcoverage) = @_; return $self->_get_AlignFeatures($logic_name, $score, $dbtype, $hcoverage, 'DnaAlignFeature'); } =head2 get_all_ProteinAlignFeatures Arg [1] : (optional) string $logic_name The name of the analysis performed on the protein align features to obtain. Arg [2] : (optional) float $score The mimimum score of the features to retrieve Arg [3] : (optional) string $dbtype The name of an attached database to retrieve features from instead. Arg [4] : (optional) float hcoverage The minimum hcoverage od the featurs to retrieve Example : @dna_pep_align_feats = @{$slice->get_all_ProteinAlignFeatures}; Description: Retrieves the DnaPepAlignFeatures which overlap this slice with logic name $logic_name and with score above $score. If $logic_name is not defined features of all logic names are retrieved. If $score is not defined features of all scores are retrieved. Returntype : listref of Bio::EnsEMBL::DnaPepAlignFeatures Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_ProteinAlignFeatures { my ($self, $logic_name, $score, $dbtype, $hcoverage) = @_; return $self->_get_AlignFeatures($logic_name, $score, $dbtype, $hcoverage, 'ProteinAlignFeature'); } =head2 _get_AlignFeatures Arg [1] : (optional) string $logic_name The name of the analysis performed on the protein align features to obtain. Arg [2] : (optional) float $score The mimimum score of the features to retrieve Arg [3] : (optional) string $dbtype The name of an attached database to retrieve features from instead. Arg [4] : (optional) float hcoverage The minimum hcoverage od the featurs to retrieve Arg [5] : string $align_type The type of adaptor to retrieve alignments from. Must be an BaseAlignFeature derived class Description: Generic method which deals with the retrieval of either AlignFeature adaptor and allows you to switch the adaptor values are retrieved from. =cut sub _get_AlignFeatures { my ($self, $logic_name, $score, $dbtype, $hcoverage, $align_type) = @_; throw "No align_type given" unless $align_type; if(my $adaptor = $self->_get_CoreAdaptor($align_type, $dbtype)) { if(defined($score) and defined ($hcoverage)){ warning "Cannot specify score and hcoverage when querying for $align_type. Using score only"; } if(defined($score)){ return $adaptor->fetch_all_by_Slice_and_score($self,$score, $logic_name); } return $adaptor->fetch_all_by_Slice_and_hcoverage($self, $hcoverage, $logic_name); } return []; } =head2 get_all_SimilarityFeatures Arg [1] : (optional) string $logic_name the name of the analysis performed on the features to retrieve Arg [2] : (optional) float $score the lower bound of the score of the features to be retrieved Example : @feats = @{$slice->get_all_SimilarityFeatures}; Description: Retrieves all dna_align_features and protein_align_features with analysis named $logic_name and with score above $score. It is probably faster to use get_all_ProteinAlignFeatures or get_all_DnaAlignFeatures if a sepcific feature type is desired. If $logic_name is not defined features of all logic names are retrieved. If $score is not defined features of all scores are retrieved. Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_SimilarityFeatures { my ($self, $logic_name, $score) = @_; my @out = (); push @out, @{$self->get_all_ProteinAlignFeatures($logic_name, $score) }; push @out, @{$self->get_all_DnaAlignFeatures($logic_name, $score) }; return \@out; } =head2 get_all_SimpleFeatures Arg [1] : (optional) string $logic_name The name of the analysis performed on the simple features to obtain. Arg [2] : (optional) float $score The mimimum score of the features to retrieve Example : @simple_feats = @{$slice->get_all_SimpleFeatures}; Description: Retrieves the SimpleFeatures which overlap this slice with logic name $logic_name and with score above $score. If $logic_name is not defined features of all logic names are retrieved. If $score is not defined features of all scores are retrieved. Returntype : listref of Bio::EnsEMBL::SimpleFeatures Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_SimpleFeatures { my ($self, $logic_name, $score, $dbtype) = @_; if(my $adaptor = $self->_get_CoreAdaptor('SimpleFeature', $dbtype)) { return $adaptor->fetch_all_by_Slice_and_score($self, $score, $logic_name); } return []; } =head2 get_all_RepeatFeatures Arg [1] : (optional) string $logic_name The name of the analysis performed on the repeat features to obtain. Arg [2] : (optional) string/array $repeat_type Limits features returned to those of the specified repeat_type. Can specify a single value or an array reference to limit by more than one Arg [3] : (optional) string $db Key for database e.g. core/vega/cdna/.... Example : @repeat_feats = @{$slice->get_all_RepeatFeatures(undef,'Type II Transposons')}; Description: Retrieves the RepeatFeatures which overlap with logic name $logic_name and with score above $score. If $logic_name is not defined features of all logic names are retrieved. Returntype : listref of Bio::EnsEMBL::RepeatFeatures Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_RepeatFeatures { my ($self, $logic_name, $repeat_type, $dbtype) = @_; if(my $adaptor = $self->_get_CoreAdaptor('RepeatFeature', $dbtype)) { return $adaptor->fetch_all_by_Slice($self, $logic_name, $repeat_type); } return []; } =head2 get_all_LD_values Arg [1] : (optional) Bio::EnsEMBL::Variation::Population $population Description : returns all LD values on this slice. This function will only work correctly if the variation database has been attached to the core database. If the argument is passed, will return the LD information in that population ReturnType : Bio::EnsEMBL::Variation::LDFeatureContainer Exceptions : none Caller : contigview, snpview Status : Stable =cut sub get_all_LD_values { my $self = shift; my $population = shift; my $ld_adaptor = $self->_get_VariationAdaptor('LDFeatureContainer'); if($ld_adaptor) { return $ld_adaptor->fetch_by_Slice($self,$population); } return []; } =head2 _get_VariationFeatureAdaptor Shortcut method here because VariationFeature is an often requested adaptor type. =cut sub _get_VariationFeatureAdaptor { my ($self, $dbtype) = @_; return $self->_get_VariationAdaptor('VariationFeature', $dbtype); } =head2 _get_StructuralVariationFeatureAdaptor Shortcut method here because StructuralVariationFeature is an often requested adaptor type. =cut sub _get_StructuralVariationFeatureAdaptor { my ($self, $dbtype) = @_; return $self->_get_VariationAdaptor('StructuralVariationFeature', $dbtype); } =head2 _get_VariationAdaptor Arg [1] : String object_type to retrieve an adaptor for Arg [2] : String dbtype to search for the given adaptor in. Defaults to variation Description : Searches for the specified adaptor in the Registry and returns it. Otherwise it will return nothing if the adaptor was not found ReturnType : Bio::EnsEMBL::DBSQL::BaseAdaptor derrived instance (specific to variation) Exceptions : none =cut sub _get_VariationAdaptor { my ($self, $object_type, $dbtype) = @_; # very important to do this defaulting since we *have* to assume the variation # database is called 'variation'. Using the current group will not work because # that will be something like 'core' (most likely), 'ensembl' or 'vega'. $dbtype ||= 'variation'; # Also we do not care about Registry->get_db() for variation DBs my $do_not_check_db = 1; return $self->_get_Adaptor($object_type, $dbtype, $do_not_check_db); } =head2 _get_CoreAdaptor Arg [1] : String object_type to retrieve an adaptor for Arg [2] : String dbtype to search for the given adaptor in. Defaults to core Description : Searches for the specified adaptor in the Registry and returns it. Otherwise it will return nothing if the adaptor was not found ReturnType : Bio::EnsEMBL::DBSQL::BaseAdaptor derrived instance (specific to core-like dbs) Exceptions : none =cut sub _get_CoreAdaptor { my ($self, $object_type, $dbtype) = @_; #Simple pass through return $self->_get_Adaptor($object_type, $dbtype); } =head2 _get_Adaptor Arg [1] : String object_type to retrieve an adaptor for Arg [2] : String dbtype to search for the given adaptor in Arg [3] : Boolean Turn off the checking of Registry->get_db() for your adaptor. Description : Searches for the specified adaptor in the Registry and returns it. Otherwise it will return nothing if the adaptor was not found. We consult the "special" adaptors held by Bio::EnsEMBL::Registry::get_db() method and then fall back to the normal methods of finding an adaptor. This method will warn when adaptors are missing but will never through an exception. It is up to the calling code to decide how to handle the unavailablity of an adaptor. ReturnType : Bio::EnsEMBL::DBSQL::BaseAdaptor derrived instance. Otherwise it returns nothing Exceptions : none =cut sub _get_Adaptor { my ($self, $object_type, $dbtype, $do_not_check_db) = @_; if(!$object_type) { warning('Object type is a required parameter'); return; } my $adaptor = $self->adaptor(); if(!$adaptor) { warning("Cannot get a ${object_type} adaptor without a SliceAdaptor attached to this instance of ".ref($self)); return; } my $local_db = $adaptor->db(); my $species = $local_db->species(); #First we query for the DBAdaptor using get_db(). This is a deprecated method #call but "special" adaptors can be registered via this method. We must #consult here 1st to find the possible special adaptor if(!$do_not_check_db && $dbtype) { my $db = $registry->get_db($local_db, $dbtype); if($db) { # If we got a return then use this DBAdaptor's species name, group and the given object type. # Special adaptors can have different species names $adaptor = $registry->get_adaptor($db->species(), $db->group(), $object_type); } else { #Otherwise just use the current species, dbtype and object type $adaptor = $registry->get_adaptor($species, $dbtype, $object_type); } } # Otherwise our query group is the one attached to the current adaptor else { #If not set use the group attached to the local adaptor $dbtype ||= $local_db->group(); $adaptor = $registry->get_adaptor($species, $dbtype, $object_type); } return $adaptor if $adaptor; warning("No adaptor could be found for the species ${species}, database type ${dbtype} and object type ${object_type}"); return; } =head2 get_all_VariationFeatures Args [1] : (optional) ArrayRef $so_terms SequenceOntology terms to limit the fetch to Args [2] : (optional) boolean $without_children Do not query using the children of the given SO terms i.e. query using the given terms directly Args [3] : (optional) ArrayRef $included_so ArrayRef of SequenceOntology which should be queried for without children. This argument allows you to combine SO terms with children from argument 1 with extra non-child SO terms. e.g. you wish to query for all protein_altering_variant (specified in argument 1) variations which would be defined by child SO terms but also wanted stop_retained_variant linked variations defined by this argument Args [4] : (optional) string $dbtype The dbtype of variation to obtain (i.e. can be different from the "variation" type). This assumes that the extra db has been added to the DBAdaptor under this name (using the DBConnection::add_db_adaptor method). Description : Returns all germline variation features on this slice. This function will only work correctly if the variation database has been attached to the core database. If $so_terms is specified, only variation features with a consequence type that matches or is an ontological child of any of the supplied terms will be returned ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Caller : contigview, snpview Status : Stable =cut sub get_all_VariationFeatures{ my ($self, $so_terms, $without_children, $included_so, $dbtype) = @_; if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_by_Slice_SO_terms($self, $so_terms, $without_children, $included_so); } return []; } =head2 get_all_somatic_VariationFeatures Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_SO_terms instead. Args [1] : (optional) ArrayRef $so_terms SequenceOntology terms to limit the fetch to Args [2] : (optional) boolean $without_children Do not query using the children of the given SO terms i.e. query using the given terms directly Args [3] : (optional) ArrayRef $included_so ArrayRef of SequenceOntology which should be queried for without children. This argument allows you to combine SO terms with children from argument 1 with extra non-child SO terms. e.g. you wish to query for all protein_altering_variant (specified in argument 1) variations which would be defined by child SO terms but also wanted stop_retained_variant linked variations defined by this argument Args [4] : (optional) string $dbtype The dbtype of variation to obtain (i.e. can be different from the "variation" type). This assumes that the extra db has been added to the DBAdaptor under this name (using the DBConnection::add_db_adaptor method). Description : Returns all somatic variation features on this slice. This function will only work correctly if the variation database has been attached to the core database. ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Status : Stable =cut sub get_all_somatic_VariationFeatures { my ($self, $so_terms, $without_children, $included_so, $dbtype) = @_; deprecate('get_all_somatic_VariationFeatures is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_SO_terms instead.'); if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_somatic_by_Slice_SO_terms($self, $so_terms, $without_children, $included_so); } return []; } =head2 get_all_somatic_VariationFeatures_by_source Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_Source instead. Arg [1] : string $source [optional] The name of the source to query for Arg [2] : string $dbtype [optional] The dbtype of variation to obtain (i.e. can be different from the "variation" type). This assumes that the extra db has been added to the DBAdaptor under this name (using the DBConnection::add_db_adaptor method). Description : Returns all somatic variation features, from a defined source name (e.g.'COSMIC'), on this slice. This function will only work correctly if the variation database has been attached to the core database. ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Status : Stable =cut sub get_all_somatic_VariationFeatures_by_source { my ($self, $source, $dbtype) = @_; deprecate('get_all_somatic_VariationFeatures_by_source is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_by_Slice_Source instead.'); my $constraint = (defined($source)) ? " s.name='$source' " : undef; if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_somatic_by_Slice_constraint($self, $constraint); } return []; } =head2 get_all_somatic_VariationFeatures_with_phenotype Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_with_phenotype_by_Slice instead. Arg [1] : $variation_feature_source [optional] Arg [2] : $phenotype_source [optional] Arg [3] : $phenotype_name [optional] Arg [4] : string $dbtype [optional] The dbtype of variation to obtain (i.e. can be different from the "variation" type). This assumes that the extra db has been added to the DBAdaptor under this name (using the DBConnection::add_db_adaptor method). Description : returns all somatic variation features on this slice associated with a phenotype. (see get_all_VariationFeatures_with_phenotype for further documentation) ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Status : Stable =cut sub get_all_somatic_VariationFeatures_with_phenotype { my ($self, $source, $p_source, $phenotype, $dbtype) = @_; deprecate('get_all_somatic_VariationFeatures_with_phenotype is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_somatic_with_phenotype_by_Slice instead.'); if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_somatic_with_phenotype_by_Slice($self, $source, $p_source, $phenotype); } return []; } =head2 get_all_VariationFeatures_by_Population Deprecated. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_Population instead. Arg [1] : Bio::EnsEMBL::Variation::Population Arg [2] : $minimum_frequency [optional] Arg [3] : string $dbtype [optional] The dbtype of variation to obtain (i.e. can be different from the "variation" type). This assumes that the extra db has been added to the DBAdaptor under this name (using the DBConnection::add_db_adaptor method). Example : $pop = $pop_adaptor->fetch_by_dbID(659); @vfs = @{$slice->get_all_VariationFeatures_by_Population($pop,$slice)}; Description : Retrieves all variation features in a slice which are stored for a specified population. If $minimum_frequency is supplied, only variations with a minor allele frequency (MAF) greater than $minimum_frequency will be returned. Returntype : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : throw on incorrect argument Caller : general Status : At Risk =cut sub get_all_VariationFeatures_by_Population { my ($self, $minimum_frequency, $dbtype) = @_; deprecate('get_all_VariationFeatures_by_Population is deprecated and will be removed in e95. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_Population instead.'); if (my $vf_adaptor = $self->_get_VariationFeatureAdaptor($dbtype)) { return $vf_adaptor->fetch_all_by_Slice_Population($self, $minimum_frequency); } return []; } =head2 get_all_Genes Arg [1] : (optional) string $logic_name The name of the analysis used to generate the genes to retrieve Arg [2] : (optional) string $dbtype The dbtype of genes to obtain. This assumes that the db has been added to the DBAdaptor under this name (using the DBConnection::add_db_adaptor method). Arg [3] : (optional) boolean $load_transcripts If set to true, transcripts will be loaded immediately rather than being lazy-loaded on request. This will result in a significant speed up if the Transcripts and Exons are going to be used (but a slow down if they are not). Arg [4] : (optional) string $source The source of the genes to retrieve. Arg [5] : (optional) string $biotype The biotype of the genes to retrieve. Example : @genes = @{$slice->get_all_Genes}; Description: Retrieves all genes that overlap this slice, including those on the reverse strand. Returntype : listref of Bio::EnsEMBL::Genes Exceptions : none Caller : none Status : Stable =cut sub get_all_Genes{ my ($self, $logic_name, $dbtype, $load_transcripts, $source, $biotype) = @_; if(my $adaptor = $self->_get_CoreAdaptor('Gene', $dbtype)) { return $adaptor->fetch_all_by_Slice( $self, $logic_name, $load_transcripts, $source, $biotype); } return []; } =head2 get_all_Genes_by_type Arg [1] : string $type The biotype of genes wanted. Arg [2] : (optional) string $logic_name Arg [3] : (optional) boolean $load_transcripts If set to true, transcripts will be loaded immediately rather than being lazy-loaded on request. This will result in a significant speed up if the Transcripts and Exons are going to be used (but a slow down if they are not). Example : @genes = @{$slice->get_all_Genes_by_type('protein_coding', 'ensembl')}; Description: Retrieves genes that overlap this slice of biotype $type. This is primarily used by the genebuilding code when several biotypes of genes are used. The logic name is the analysis of the genes that are retrieved. If not provided all genes will be retrieved instead. Both positive and negative strand Genes will be returned. Returntype : listref of Bio::EnsEMBL::Genes Exceptions : none Caller : genebuilder, general Status : Stable =cut sub get_all_Genes_by_type { my ($self, $type, $logic_name, $load_transcripts) = @_; return $self->get_all_Genes($logic_name, undef, $load_transcripts, undef, $type); } =head2 get_all_Genes_by_source Arg [1] : string source Arg [2] : (optional) boolean $load_transcripts If set to true, transcripts will be loaded immediately rather than being lazy-loaded on request. This will result in a significant speed up if the Transcripts and Exons are going to be used (but a slow down if they are not). Example : @genes = @{$slice->get_all_Genes_by_source('ensembl')}; Description: Retrieves genes that overlap this slice of source $source. Strand of the Slice does not affect the result. Returntype : listref of Bio::EnsEMBL::Genes Exceptions : none Caller : general Status : Stable =cut sub get_all_Genes_by_source { my ($self, $source, $load_transcripts) = @_; return $self->get_all_Genes(undef, undef, $load_transcripts, $source); } =head2 get_all_Transcripts Arg [1] : (optional) boolean $load_exons If set to true exons will not be lazy-loaded but will instead be loaded right away. This is faster if the exons are actually going to be used right away. Arg [2] : (optional) string $logic_name the logic name of the type of features to obtain Arg [3] : (optional) string $db_type Example : @transcripts = @{$slice->get_all_Transcripts)_}; Description: Gets all transcripts which overlap this slice. If you want to specify a particular analysis or type, then you are better off using get_all_Genes or get_all_Genes_by_type and iterating through the transcripts of each gene. Strand of the Slice is ignored. Returntype : reference to a list of Bio::EnsEMBL::Transcripts Exceptions : none Caller : general Status : Stable =cut sub get_all_Transcripts { my ($self, $load_exons, $logic_name, $dbtype, $source, $biotype) = @_; if(my $adaptor = $self->_get_CoreAdaptor('Transcript', $dbtype)) { return $adaptor->fetch_all_by_Slice($self, $load_exons, $logic_name, undef, $source, $biotype); } return []; } =head2 get_all_Transcripts_by_type Arg [1] : string $type The biotype of transcripts wanted. Arg [2] : (optional) string $logic_name Arg [3] : (optional) boolean $load_exons If set to true exons will not be lazy-loaded but will instead be loaded right away. This is faster if the exons are actually going to be used right away. Example : @transcripts = @{$slice->get_all_Transcripts_by_type('protein_coding', 'ensembl')}; Description: Retrieves transcripts that overlap this slice of biotype $type. This is primarily used by the genebuilding code when several biotypes of transcripts are used. The logic name is the analysis of the transcripts that are retrieved. If not provided all transcripts will be retrieved instead. Both positive and negative strand transcripts will be returned. Returntype : listref of Bio::EnsEMBL::Transcripts Exceptions : none Caller : genebuilder, general Status : Stable =cut sub get_all_Transcripts_by_type { my ($self, $biotype, $logic_name, $load_exons) = @_; return $self->get_all_Transcripts($load_exons, $logic_name, undef, undef, $biotype); } =head2 get_all_Transcripts_by_source Arg [1] : string source Arg [2] : (optional) boolean $load_exons If set to true exons will not be lazy-loaded but will instead be loaded right away. This is faster if the exons are actually going to be used right away. Example : @transcripts = @{$slice->get_all_Transcripts_by_source('ensembl')}; Description: Retrieves transcripts that overlap this slice of source $source. Strand of the Slice does not affect the result. Returntype : listref of Bio::EnsEMBL::Transcripts Exceptions : none Caller : general Status : Stable =cut sub get_all_Transcripts_by_source { my ($self, $source, $load_exons) = @_; return $self->get_all_Transcripts($load_exons, undef, undef, $source); } =head2 get_all_Exons Arg [1] : none Example : @exons = @{$slice->get_all_Exons}; Description: Gets all exons which overlap this slice. Note that these exons will not be associated with any transcripts, so this may not be terribly useful. Returntype : reference to a list of Bio::EnsEMBL::Exons Exceptions : none Caller : general Status : Stable =cut sub get_all_Exons { my $self = shift; if(!$self->adaptor()) { warning('Cannot get Exons without attached adaptor'); return []; } return $self->adaptor->db->get_ExonAdaptor->fetch_all_by_Slice($self); } =head2 get_all_KaryotypeBands Arg [1] : none Example : @kary_bands = @{$slice->get_all_KaryotypeBands}; Description: Retrieves the karyotype bands which this slice overlaps. Returntype : listref oif Bio::EnsEMBL::KaryotypeBands Exceptions : none Caller : general, contigview Status : Stable =cut sub get_all_KaryotypeBands { my ($self) = @_; if (my $adaptor = $self->_get_CoreAdaptor('KaryotypeBand')) { return $adaptor->fetch_all_by_Slice($self); } return []; } =head2 get_repeatmasked_seq Arg [1] : listref of strings $logic_names (optional) Arg [2] : int $soft_masking_enable (optional) Arg [3] : hash reference $not_default_masking_cases (optional, default is {}) The values are 0 or 1 for hard and soft masking respectively The keys of the hash should be of 2 forms "repeat_class_" . $repeat_consensus->repeat_class, e.g. "repeat_class_SINE/MIR" "repeat_name_" . $repeat_consensus->name e.g. "repeat_name_MIR" depending on which base you want to apply the not default masking either the repeat_class or repeat_name. Both can be specified in the same hash at the same time, but in that case, repeat_name setting has priority over repeat_class. For example, you may have hard masking as default, and you may want soft masking of all repeat_class SINE/MIR, but repeat_name AluSp (which are also from repeat_class SINE/MIR). Your hash will be something like {"repeat_class_SINE/MIR" => 1, "repeat_name_AluSp" => 0} Example : $rm_slice = $slice->get_repeatmasked_seq(); $softrm_slice = $slice->get_repeatmasked_seq(['RepeatMask'],1); Description: Returns Bio::EnsEMBL::Slice that can be used to create repeat masked sequence instead of the regular sequence. Sequence returned by this new slice will have repeat regions hardmasked by default (sequence replaced by N) or or soft-masked when arg[2] = 1 (sequence in lowercase) Will only work with database connection to get repeat features. Returntype : Bio::EnsEMBL::RepeatMaskedSlice Exceptions : none Caller : general Status : Stable =cut sub get_repeatmasked_seq { my ($self,$logic_names,$soft_mask,$not_default_masking_cases) = @_; return Bio::EnsEMBL::RepeatMaskedSlice->new (-START => $self->{'start'}, -END => $self->{'end'}, -STRAND => $self->{'strand'}, -ADAPTOR => $self->adaptor(), -SEQ => $self->{'seq'}, -SEQ_REGION_NAME => $self->{'seq_region_name'}, -SEQ_REGION_LENGTH => $self->{'seq_region_length'}, -COORD_SYSTEM => $self->{'coord_system'}, -REPEAT_MASK => $logic_names, -SOFT_MASK => $soft_mask, -NOT_DEFAULT_MASKING_CASES => $not_default_masking_cases); } =head2 _mask_features Arg [1] : reference to a string $dnaref Arg [2] : array_ref $repeats reference to a list Bio::EnsEMBL::RepeatFeature give the list of coordinates to replace with N or with lower case Arg [3] : int $soft_masking_enable (optional) Arg [4] : hash reference $not_default_masking_cases (optional, default is {}) The values are 0 or 1 for hard and soft masking respectively The keys of the hash should be of 2 forms "repeat_class_" . $repeat_consensus->repeat_class, e.g. "repeat_class_SINE/MIR" "repeat_name_" . $repeat_consensus->name e.g. "repeat_name_MIR" depending on which base you want to apply the not default masking either the repeat_class or repeat_name. Both can be specified in the same hash at the same time, but in that case, repeat_name setting has priority over repeat_class. For example, you may have hard masking as default, and you may want soft masking of all repeat_class SINE/MIR, but repeat_name AluSp (which are also from repeat_class SINE/MIR). Your hash will be something like {"repeat_class_SINE/MIR" => 1, "repeat_name_AluSp" => 0} Example : none Description: replaces string positions described in the RepeatFeatures with Ns (default setting), or with the lower case equivalent (soft masking). The reference to a dna string which is passed is changed in place. Returntype : none Exceptions : none Caller : seq Status : Stable =cut sub _mask_features { my ($self,$dnaref,$repeats,$soft_mask,$not_default_masking_cases) = @_; $soft_mask = 0 unless (defined $soft_mask); $not_default_masking_cases = {} unless (defined $not_default_masking_cases); # explicit CORE::length call, to avoid any confusion with the Slice # length method my $dnalen = CORE::length($$dnaref); REP:foreach my $old_f (@{$repeats}) { my $f = $old_f->transfer( $self ); my $start = $f->start; my $end = $f->end; my $length = ($end - $start) + 1; # check if we get repeat completely outside of expected slice range if ($end < 1 || $start > $dnalen) { # warning("Unexpected: Repeat completely outside slice coordinates."); next REP; } # repeat partly outside slice range, so correct # the repeat start and length to the slice size if needed if ($start < 1) { $start = 1; $length = ($end - $start) + 1; } # repeat partly outside slice range, so correct # the repeat end and length to the slice size if needed if ($end > $dnalen) { $end = $dnalen; $length = ($end - $start) + 1; } $start--; my $padstr; # if we decide to define masking on the base of the repeat_type, we'll need # to add the following, and the other commented line few lines below. my $rc_class; my $rc_name; if ($f->isa('Bio::EnsEMBL::RepeatFeature')) { $rc_class = "repeat_class_" . $f->repeat_consensus->repeat_class; $rc_name = "repeat_name_" . $f->repeat_consensus->name; } my $masking_type; $masking_type = $not_default_masking_cases->{$rc_class} if (defined $not_default_masking_cases->{$rc_class}); $masking_type = $not_default_masking_cases->{$rc_name} if (defined $not_default_masking_cases->{$rc_name}); $masking_type = $soft_mask unless (defined $masking_type); if ($masking_type) { $padstr = lc substr ($$dnaref,$start,$length); } else { $padstr = 'N' x $length; } substr ($$dnaref,$start,$length) = $padstr; } } =head2 get_all_SearchFeatures Arg [1] : scalar $ticket_ids Example : $slice->get_all_SearchFeatures('BLA_KpUwwWi5gY'); Description: Retrieves all search features for stored blast results for the ticket that overlap this slice Returntype : listref of Bio::EnsEMBL::SeqFeatures Exceptions : none Caller : general (webby!) Status : Stable =cut sub get_all_SearchFeatures { my $self = shift; my $ticket = shift; local $_; unless($ticket) { throw("ticket argument is required"); } if(!$self->adaptor()) { warning("Cannot get SearchFeatures without an attached adaptor"); return []; } my $sfa = $self->adaptor()->db()->get_db_adaptor('blast'); my $offset = $self->start-1; my $features = $sfa ? $sfa->get_all_SearchFeatures($ticket, $self->seq_region_name, $self->start, $self->end) : []; foreach( @$features ) { $_->start( $_->start - $offset ); $_->end( $_->end - $offset ); }; return $features; } =head2 get_all_AssemblyExceptionFeatures Example : $slice->get_all_AssemblyExceptionFeatures(); Description: Retrieves all misc features which overlap this slice. If a set code is provided only features which are members of the requested set are returned. Returntype : listref of Bio::EnsEMBL::AssemblyExceptionFeatures Exceptions : none Caller : general Status : Stable =cut sub get_all_AssemblyExceptionFeatures { my ($self) = @_; if(my $adaptor = $self->_get_CoreAdaptor('AssemblyExceptionFeature')) { return $adaptor->fetch_all_by_Slice($self); } return []; } =head2 get_all_MiscFeatures Arg [1] : string $set (optional) Arg [2] : string $database (optional) Example : $slice->get_all_MiscFeatures('cloneset'); Description: Retrieves all misc features which overlap this slice. If a set code is provided only features which are members of the requested set are returned. Returntype : listref of Bio::EnsEMBL::MiscFeatures Exceptions : none Caller : general Status : Stable =cut sub get_all_MiscFeatures { my ($self, $misc_set, $dbtype) = @_; if(my $adaptor = $self->_get_CoreAdaptor('MiscFeature', $dbtype)) { if($misc_set) { return $adaptor->fetch_all_by_Slice_and_set_code($self,$misc_set); } return $adaptor->fetch_all_by_Slice($self); } return []; } =head2 get_all_MarkerFeatures Arg [1] : (optional) string logic_name The logic name of the marker features to retrieve Arg [2] : (optional) int $priority Lower (exclusive) priority bound of the markers to retrieve Arg [3] : (optional) int $map_weight Upper (exclusive) priority bound of the markers to retrieve Example : my @markers = @{$slice->get_all_MarkerFeatures(undef,50, 2)}; Description: Retrieves all markers which lie on this slice fulfilling the specified map_weight and priority parameters (if supplied). Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures Exceptions : none Caller : contigview, general Status : Stable =cut sub get_all_MarkerFeatures { my ($self, $logic_name, $priority, $map_weight) = @_; if(my $adaptor = $self->_get_CoreAdaptor('MarkerFeature')) { return $adaptor->fetch_all_by_Slice_and_priority($self, $priority, $map_weight, $logic_name); } return []; } =head2 get_MarkerFeatures_by_Name Arg [1] : string marker Name The name (synonym) of the marker feature(s) to retrieve Example : my @markers = @{$slice->get_MarkerFeatures_by_Name('z1705')}; Description: Retrieves all markers with this ID Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures Exceptions : none Caller : contigview, general Status : Stable =cut sub get_MarkerFeatures_by_Name { my ($self, $name) = @_; if(my $adaptor = $self->_get_CoreAdaptor('MarkerFeature')) { return $adaptor->fetch_all_by_Slice_and_MarkerName($self, $name); } return []; } =head2 get_all_compara_DnaAlignFeatures Arg [1] : string $qy_species The name of the species to retrieve similarity features from Arg [2] : string $qy_assembly The name of the assembly to retrieve similarity features from Arg [3] : string $type The type of the alignment to retrieve similarity features from Arg [4] : compara dbadptor to use. Example : $fs = $slc->get_all_compara_DnaAlignFeatures('Mus musculus', 'MGSC3', 'WGA'); Description: Retrieves a list of DNA-DNA Alignments to the species specified by the $qy_species argument. The compara database must be attached to the core database for this call to work correctly. As well the compara database must have the core dbadaptors for both this species, and the query species added to function correctly. Returntype : reference to a list of Bio::EnsEMBL::DnaDnaAlignFeatures Exceptions : warning if compara database is not available Caller : contigview Status : Stable =cut sub get_all_compara_DnaAlignFeatures { my ($self, $qy_species, $qy_assembly, $alignment_type, $compara_db) = @_; if(!$self->adaptor()) { warning("Cannot retrieve DnaAlignFeatures without attached adaptor"); return []; } unless($qy_species && $alignment_type # && $qy_assembly ) { throw("Query species and assembly and alignmemt type arguments are required"); } if(!defined($compara_db)){ $compara_db = Bio::EnsEMBL::Registry->get_DBAdaptor("compara", "compara"); } unless($compara_db) { warning("Compara database must be attached to core database or passed ". "as an argument to " . "retrieve compara information"); return []; } my $dafa = $compara_db->get_DnaAlignFeatureAdaptor; return $dafa->fetch_all_by_Slice($self, $qy_species, $qy_assembly, $alignment_type); } =head2 get_all_compara_Syntenies Arg [1] : string $query_species e.g. "Mus_musculus" or "Mus musculus" Arg [2] : string $method_link_type, default is "SYNTENY" Arg [3] : compara dbadaptor to use. Description: gets all the compara syntenyies for a specfic species Returns : arrayref of Bio::EnsEMBL::Compara::SyntenyRegion Status : Stable =cut sub get_all_compara_Syntenies { my ($self, $qy_species, $method_link_type, $compara_db) = @_; if(!$self->adaptor()) { warning("Cannot retrieve features without attached adaptor"); return []; } unless($qy_species) { throw("Query species and assembly arguments are required"); } unless (defined $method_link_type) { $method_link_type = "SYNTENY"; } if(!defined($compara_db)){ $compara_db = Bio::EnsEMBL::Registry->get_DBAdaptor("compara", "compara"); } unless($compara_db) { warning("Compara database must be attached to core database or passed ". "as an argument to " . "retrieve compara information"); return []; } my $gdba = $compara_db->get_GenomeDBAdaptor(); my $mlssa = $compara_db->get_MethodLinkSpeciesSetAdaptor(); my $sra = $compara_db->get_SyntenyRegionAdaptor(); my $this_gdb = $gdba->fetch_by_core_DBAdaptor($self->adaptor()->db()); my $query_gdb = $gdba->fetch_by_registry_name($qy_species); my $mlss; if($this_gdb eq $query_gdb) { $mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($method_link_type, [$this_gdb]); } else { $mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($method_link_type, [$this_gdb, $query_gdb]); } return $sra->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $self); } =head2 get_all_Haplotypes Arg [1] : (optional) boolean $lite_flag if true lightweight haplotype objects are used Example : @haplotypes = $slice->get_all_Haplotypes; Description: Retrieves all of the haplotypes on this slice. Only works if the haplotype adaptor has been attached to the core adaptor via $dba->add_db_adaptor('haplotype', $hdba); Returntype : listref of Bio::EnsEMBL::External::Haplotype::Haplotypes Exceptions : warning is Haplotype database is not available Caller : contigview, general Status : Stable =cut sub get_all_Haplotypes { my($self, $lite_flag) = @_; if(!$self->adaptor()) { warning("Cannot retrieve features without attached adaptor"); return []; } my $haplo_db = $self->adaptor->db->get_db_adaptor('haplotype'); unless($haplo_db) { warning("Haplotype database must be attached to core database to " . "retrieve haplotype information" ); return []; } my $haplo_adaptor = $haplo_db->get_HaplotypeAdaptor; my $haplotypes = $haplo_adaptor->fetch_all_by_Slice($self, $lite_flag); return $haplotypes; } sub get_all_DASFactories { my $self = shift; return [ $self->adaptor()->db()->_each_DASFeatureFactory ]; } sub get_all_DASFeatures_dsn { my ($self, $source_type, $dsn) = @_; if(!$self->adaptor()) { warning("Cannot retrieve features without attached adaptor"); return []; } my @X = grep { $_->adaptor->dsn eq $dsn } $self->adaptor()->db()->_each_DASFeatureFactory; return [ $X[0]->fetch_all_Features( $self, $source_type ) ]; } =head2 get_all_DAS_Features Arg [1] : none Example : $features = $slice->get_all_DASFeatures; Description: Retrieves a hash reference to a hash of DAS feature sets, keyed by the DNS, NOTE the values of this hash are an anonymous array containing: (1) a pointer to an array of features; (2) a pointer to the DAS stylesheet Returntype : hashref of Bio::SeqFeatures Exceptions : ? Caller : webcode Status : Stable =cut sub get_all_DAS_Features{ my ($self) = @_; $self->{_das_features} ||= {}; # Cache $self->{_das_styles} ||= {}; # Cache $self->{_das_segments} ||= {}; # Cache my %das_features; my %das_styles; my %das_segments; my $slice = $self; foreach my $dasfact( @{$self->get_all_DASFactories} ){ my $dsn = $dasfact->adaptor->dsn; my $name = $dasfact->adaptor->name; # my $type = $dasfact->adaptor->type; my $url = $dasfact->adaptor->url; my ($type) = $dasfact->adaptor->mapping; if (ref $type eq 'ARRAY') { $type = shift @$type; } $type ||= $dasfact->adaptor->type; # Construct a cache key : SOURCE_URL/TYPE # Need the type to handle sources that serve multiple types of features my $key = join('/', $name, $type); if( $self->{_das_features}->{$key} ){ # Use cached $das_features{$name} = $self->{_das_features}->{$key}; $das_styles{$name} = $self->{_das_styles}->{$key}; $das_segments{$name} = $self->{_das_segments}->{$key}; } else { # Get fresh data my ($featref, $styleref, $segref) = $dasfact->fetch_all_Features( $slice, $type ); $self->{_das_features}->{$key} = $featref; $self->{_das_styles}->{$key} = $styleref; $self->{_das_segments}->{$key} = $segref; $das_features{$name} = $featref; $das_styles{$name} = $styleref; $das_segments{$name} = $segref; } } return (\%das_features, \%das_styles, \%das_segments); } sub get_all_DASFeatures{ my ($self, $source_type) = @_; if(!$self->adaptor()) { warning("Cannot retrieve features without attached adaptor"); return []; } my %genomic_features = map { ( $_->adaptor->dsn => [ $_->fetch_all_Features($self, $source_type) ] ) } $self->adaptor()->db()->_each_DASFeatureFactory; return \%genomic_features; } sub old_get_all_DASFeatures{ my ($self,@args) = @_; if(!$self->adaptor()) { warning("Cannot retrieve features without attached adaptor"); return []; } my %genomic_features = map { ( $_->adaptor->dsn => [ $_->fetch_all_by_Slice($self) ] ) } $self->adaptor()->db()->_each_DASFeatureFactory; return \%genomic_features; } =head2 get_all_ExternalFeatures Arg [1] : (optional) string $track_name If specified only features from ExternalFeatureAdaptors with the track name $track_name are retrieved. If not set, all features from every ExternalFeatureAdaptor are retrieved. Example : @x_features = @{$slice->get_all_ExternalFeatures} Description: Retrieves features on this slice from external feature adaptors Returntype : listref of Bio::SeqFeatureI implementing objects in slice coordinates Exceptions : none Caller : general Status : Stable =cut sub get_all_ExternalFeatures { my ($self, $track_name) = @_; if(!$self->adaptor()) { warning("Cannot retrieve features without attached adaptor"); return []; } my $features = []; my $xfa_hash = $self->adaptor->db->get_ExternalFeatureAdaptors; my @xf_adaptors = (); if($track_name) { #use a specific adaptor if(exists $xfa_hash->{$track_name}) { push @xf_adaptors, $xfa_hash->{$track_name}; } } else { #use all of the adaptors push @xf_adaptors, values %$xfa_hash; } foreach my $xfa (@xf_adaptors) { push @$features, @{$xfa->fetch_all_by_Slice($self)}; } return $features; } =head2 get_all_DitagFeatures Arg [1] : (optional) string ditag type Arg [1] : (optional) string logic_name Example : @dna_dna_align_feats = @{$slice->get_all_DitagFeatures}; Description: Retrieves the DitagFeatures of a specific type which overlap this slice. If type is not defined, all features are retrieved. Strandedness of the Slice is ignored. Returntype : listref of Bio::EnsEMBL::DitagFeatures Exceptions : warning if slice does not have attached adaptor Caller : general Status : Stable =cut sub get_all_DitagFeatures { my ($self, $type, $logic_name) = @_; if(my $adaptor = $self->_get_CoreAdaptor('DitagFeature')) { return $adaptor->fetch_all_by_Slice($self, $type, $logic_name); } return []; } # GENERIC FEATURES (See DBAdaptor.pm) =head2 get_generic_features Arg [1] : (optional) List of names of generic feature types to return. If no feature names are given, all generic features are returned. Example : my %features = %{$slice->get_generic_features()}; Description: Gets generic features via the generic feature adaptors that have been added via DBAdaptor->add_GenricFeatureAdaptor (if any) Returntype : Hash of named features. Exceptions : none Caller : none Status : Stable =cut sub get_generic_features { my ($self, @names) = @_; if(!$self->adaptor()) { warning('Cannot retrieve features without attached adaptor'); return []; } my $db = $self->adaptor()->db(); my %features = (); # this will hold the results # get the adaptors for each feature my %adaptors = %{$db->get_GenericFeatureAdaptors(@names)}; foreach my $adaptor_name (keys(%adaptors)) { my $adaptor_obj = $adaptors{$adaptor_name}; # get the features and add them to the hash my $features_ref = $adaptor_obj->fetch_all_by_Slice($self); # add each feature to the hash to be returned foreach my $feature (@$features_ref) { $features{$adaptor_name} = $feature; } } return \%features; } =head2 project_to_slice Arg [1] : Slice to project to. Example : my $chr_projection = $clone_slice->project_to_slice($chrom_slice); foreach my $segment ( @$chr_projection ){ $chr_slice = $segment->to_Slice(); print $clone_slice->seq_region_name(). ':'. $segment->from_start(). '-'. $segment->from_end(). ' -> '.$chr_slice->seq_region_name(). ':'. $chr_slice->start(). '-'.$chr_slice->end(). $chr_slice->strand(). " length: ".($chr_slice->end()-$chr_slice->start()+1). "\n"; } Description: Projection of slice to another specific slice. Needed for where we have multiple mappings and we want to state which one to project to. Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which can also be used as [$start,$end,$slice] triplets. Exceptions : none Caller : none Status : At Risk =cut sub project_to_slice { my $self = shift; my $to_slice = shift; throw('Slice argument is required') if(!$to_slice); my $slice_adaptor = $self->adaptor(); if(!$slice_adaptor) { warning("Cannot project without attached adaptor."); return []; } my $mapper_aptr = $slice_adaptor->db->get_AssemblyMapperAdaptor(); my $cs = $to_slice->coord_system(); my $slice_cs = $self->coord_system(); my $to_slice_id = $to_slice->get_seq_region_id; my @projection; # decompose this slice into its symlinked components. # this allows us to handle haplotypes and PARs my $normal_slice_proj = $slice_adaptor->fetch_normalized_slice_projection($self); foreach my $segment (@$normal_slice_proj) { my $normal_slice = $segment->[2]; $slice_cs = $normal_slice->coord_system(); my $asma = $self->adaptor->db->get_AssemblyMapperAdaptor(); my $asm_mapper = $asma->fetch_by_CoordSystems($slice_cs, $cs); next unless defined $asm_mapper; # perform the mapping between this slice and the requested system my @coords = $asm_mapper->map($normal_slice->seq_region_name(), $normal_slice->start(), $normal_slice->end(), $normal_slice->strand(), $slice_cs, undef, $to_slice, 1); #construct a projection from the mapping results and return it foreach my $coord (@coords) { my $original = $coord->{original}; my $mapped = $coord->{mapped}; # skip gaps next unless $mapped->isa('Bio::EnsEMBL::Mapper::Coordinate'); my $mapped_start = $mapped->start(); my $mapped_end = $mapped->end(); my ($current_start, $current_end); if ($self->strand == 1) { $current_start = $original->start() - $self->start + 1; $current_end = $original->end() - $self->start + 1; } else { $current_start = $self->end() - $original->end + 1; $current_end = $self->end - $original->start + 1; } # for multiple mappings only get the correct one next unless $mapped->id == $to_slice_id; my $coord_cs = $mapped->coord_system(); # If the normalised projection just ended up mapping to the # same coordinate system we were already in then we should just # return the original region. This can happen for example, if we # were on a PAR region on Y which refered to X and a projection to # 'toplevel' was requested. # if($coord_cs->equals($slice_cs)) { # # trim off regions which are not defined # return $self->_constrain_to_region(); # } # create slices for the mapped-to coord system my $slice = $slice_adaptor->fetch_by_seq_region_id($mapped->id(), $mapped_start, $mapped_end, $mapped->strand()); push @projection, bless([$current_start, $current_end, $slice], "Bio::EnsEMBL::ProjectionSegment"); } } # delete the cache as we may want to map to different set next time and old # results will be cached. $mapper_aptr->delete_cache; return \@projection; } =head2 get_all_synonyms Args [1] : String external_db_name The name of the database to retrieve the synonym for Args [2] : (optional) Integer external_db_version Optionally restrict results from external_db_name to a specific version of the the specified external database Example : my @alternative_names = @{$slice->get_all_synonyms()}; @alternative_names = @{$slice->get_all_synonyms('EMBL')}; Description: get a list of alternative names for this slice Returntype : reference to list of SeqRegionSynonym objects. Exception : none Caller : general Status : At Risk =cut sub get_all_synonyms { my ($self, $external_db_name, $external_db_version) = @_; if ( !defined( $self->{'synonym'} ) ) { my $adap = $self->adaptor->db->get_SeqRegionSynonymAdaptor(); $self->{'synonym'} = $adap->get_synonyms( $self->get_seq_region_id($self) ); } if(! $external_db_name) { return $self->{'synonym'}; } my @args = ($external_db_version) ? ($external_db_name, $external_db_version) : ($external_db_name, undef, 1); my $external_db_id = $self->adaptor->db()->get_DBEntryAdaptor()->get_external_db_id(@args); if(!$external_db_id) { my $extra = ($external_db_version) ? "and version $external_db_version " : q{}; throw "The external database $external_db_name ${extra}did not result in a valid identifier"; } return [ grep { $_->external_db_id() == $external_db_id } @{$self->{synonym}} ]; } =head2 add_synonym Args[0] : synonym. Example : $slice->add_synonym("alt_name"); Description: add an alternative name for this slice Returntype : none Exception : none Caller : general Status : At Risk =cut sub add_synonym{ my $self = shift; my $syn = shift; my $external_db_id = shift; my $adap = $self->adaptor->db->get_SeqRegionSynonymAdaptor(); if ( !defined( $self->{'synonym'} ) ) { $self->{'synonym'} = $self->get_all_synonyms(); } my $new_syn = Bio::EnsEMBL::SeqRegionSynonym->new( #-adaptor => $adap, -synonym => $syn, -external_db_id => $external_db_id, -seq_region_id => $self->get_seq_region_id($self)); push (@{$self->{'synonym'}}, $new_syn); return; } # package variable to minimize duplication my %region_so_mapping = ( 'chromosome' => 'SO:0000340', 'supercontig' => 'SO:0000148', 'scaffold' => 'SO:0000148', 'contig' => 'SO:0000149' ); =head2 feature_so_acc Example : $slice_so_acc = $slice->feature_so_acc; Description : This method returns a string containing the SO accession number of the slice, based on the coordinate system name. Returns : string (Sequence Ontology accession number) =cut sub feature_so_acc { my $self = shift; # return the region SO acc, or Slice acc return $region_so_mapping{$self->coord_system_name} // 'SO:0000001'; } =head2 feature_so_term Description: This method returns a string containing the SO term of the slice, based on the coordinate system name Define constant SEQUENCE_ONTOLOGY in classes that require it, or override it for multiple possible values for a class. Returntype : String (Sequence Ontology term) Exceptions : Thrown if caller SEQUENCE_ONTOLOGY is undefined and is not a Bio::EnsEMBL::Slice =cut sub feature_so_term { my ($self) = shift; return defined($region_so_mapping{$self->coord_system_name}) ? $self->coord_system_name : 'region'; } =head2 summary_as_hash Example : $slice_summary = $slice->summary_as_hash(); Description : Retrieves a textual summary of this slice. Returns : hashref of descriptive strings =cut sub summary_as_hash { my $self = shift; my %summary; my @aliases = map { $_->name } @{$self->slice->get_all_synonyms()}; $summary{'seq_region_name'} = $self->seq_region_name; $summary{'id'} = $self->seq_region_name; $summary{'start'} = $self->start; $summary{'end'} = $self->end; $summary{'strand'} = 0; $summary{'source'} = $self->source || $self->coord_system->version; $summary{'Alias'} = \@aliases if scalar(@aliases); $summary{'Is_circular'} = $self->is_circular ? "true" : undef; return \%summary; } sub slice { my $self = shift; return $self; } # # Bioperl Bio::PrimarySeqI methods: # =head2 id Description: Included for Bio::PrimarySeqI interface compliance (0.7) =cut sub id { name(@_); } =head2 display_id Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub display_id { name(@_); } =head2 primary_id Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub primary_id { name(@_); } =head2 desc Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub desc{ return $_[0]->coord_system->name().' '.$_[0]->seq_region_name(); } =head2 moltype Description: Included for Bio::PrimarySeqI interface compliance (0.7) =cut sub moltype { return 'dna'; } =head2 alphabet Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub alphabet { return 'dna'; } =head2 accession_number Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub accession_number { name(@_); } 1;