=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::CircularSlice - 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. =head1 METHODS =cut package Bio::EnsEMBL::CircularSlice; use vars qw(@ISA); use strict; use Bio::PrimarySeqI; use Bio::EnsEMBL::Utils::Argument qw(rearrange); use Bio::EnsEMBL::Utils::Exception qw(throw warning); use Bio::EnsEMBL::RepeatMaskedSlice; use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp); use Bio::EnsEMBL::Utils::Scalar qw( assert_ref ); use Bio::EnsEMBL::ProjectionSegment; use Bio::EnsEMBL::Registry; use Bio::EnsEMBL::DBSQL::MergedAdaptor; #use Bio::EnsEMBL::IndividualSlice; #use Bio::EnsEMBL::IndividualSliceFactory; use Bio::EnsEMBL::Mapper::RangeRegistry; use Bio::EnsEMBL::Slice; use Data::Dumper; use Scalar::Util qw(weaken isweak); my $reg = "Bio::EnsEMBL::Registry"; @ISA = qw(Bio::EnsEMBL::Slice); =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::CircularSlice->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::CircularSlice 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 ( !defined($seq_region_length) ) { $seq_region_length = $end } if ( $seq_region_length <= 0 ) { throw('SEQ_REGION_LENGTH must be > 0'); } if ( defined($coord_system) ) { assert_ref( $coord_system, 'Bio::EnsEMBL::CoordSystem' ); if ( $coord_system->is_top_level() ) { throw('Cannot create circular slice on toplevel CoordSystem.'); } } else { warning("CircularSlice without coordinate system"); } $strand ||= 1; if ( $strand != 1 && $strand != -1 ) { throw('STRAND argument must be -1 or 1'); } if ( defined($adaptor) ) { assert_ref( $adaptor, 'Bio::EnsEMBL::DBSQL::SliceAdaptor' ); } my $seq1 = { '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 }; bless $seq1, $class; $seq1->adaptor($adaptor); return $seq1; } ## end sub new =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; my ( $s, $e, $length ) = ( $self->{'start'}, $self->{'end'}, $self->{'seq_region_length'} ); if ( $s < $e ) { return ( $s + $e )/2; } my $r1 = $length - $s; my $r2 = $e; my $r = ( $r1 + $r2 )/2; my $m = $s + $r; if ( $m > $length ) { $m = $m - $length; } return $m; } =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) = @_; if ( $self->{'start'} < $self->{'end'} ) { return $self->{'end'} - $self->{'start'} + 1; } my $r1 = $self->{'seq_region_length'} - $self->{'start'}; my $r2 = $self->{'end'}; my $ln = $r1 + $r2 + 1; return $ln; } sub _split { my $self = shift; my $sl1 = Bio::EnsEMBL::CircularSlice->new( -COORD_SYSTEM => $self->{'coord_system'}, -SEQ_REGION_NAME => $self->{'seq_region_name'}, -SEQ_REGION_LENGTH => $self->{'seq_region_length'}, -START => $self->{'start'}, -END => $self->{'seq_region_length'}, -STRAND => $self->{'strand'}, -ADAPTOR => $self->adaptor() ); my $sl2 = Bio::EnsEMBL::CircularSlice->new( -COORD_SYSTEM => $self->{'coord_system'}, -SEQ_REGION_NAME => $self->{'seq_region_name'}, -SEQ_REGION_LENGTH => $self->{'seq_region_length'}, -START => 1, -END => $self->{'end'}, -STRAND => $self->{'strand'}, -ADAPTOR => $self->adaptor() ); return ($sl1, $sl2); } =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. 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(); if ( $self->{'start'} > $self->{'end'} ) { my $length = $self->{'seq_region_length'}; my ($sl1, $sl2) = $self->_split; my $seq1 = ${ $seqAdaptor->fetch_by_Slice_start_end_strand( $sl1, 1, $sl1->end - $sl1->start + 1, $sl1->strand) }; my $seq2 = ${ $seqAdaptor->fetch_by_Slice_start_end_strand( $sl2, 1, $sl2->end - $sl2->start + 1, $sl2->strand) }; return $seq1 . $seq2; } else { my $seq1 = ${ $seqAdaptor->fetch_by_Slice_start_end_strand( $self, 1, undef, 1 ) }; return $seq1; } } ## end if ( $self->adaptor() ) # no attached sequence, and no db, so just return Ns return 'N' x $self->length(); } ## end sub seq =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 ) = @_; # 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; my $length = $self->{'seq_region_length'}; if ( $self->adaptor ) { my $seqAdaptor = $self->adaptor->db->get_SequenceAdaptor(); if ( $end < $start ) { my $subseq1 = ${ $seqAdaptor->fetch_by_Slice_start_end_strand( $self, $start, $length, $strand ) }; my $subseq2 = ${ $seqAdaptor->fetch_by_Slice_start_end_strand( $self, 1, $end, $strand ) }; $subseq = $subseq1 . $subseq2; } else { $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; } ## end sub subseq =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 $new_start; my $new_end; my $sshift = $five_prime_shift; my $eshift = $three_prime_shift; if ( $self->{'strand'} != 1 ) { $eshift = $five_prime_shift; $sshift = $three_prime_shift; } $new_start = $self->{'start'} - $sshift; $new_end = $self->{'end'} + $eshift; # if($new_start > $new_end) { # if ($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 get_all_VariationFeatures Args : $filter [optional] Description:returns all variation features on this slice. This function will only work correctly if the variation database has been attached to the core database. If $filter is "genotyped" return genotyped Snps only... (nice likkle hack); ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Caller : contigview, snpview Status : At Risk : Variation database is under development. =cut sub get_all_VariationFeatures { my $self = shift; my $filter = shift; $filter ||= ''; if ( !$self->adaptor() ) { warning('Cannot get variation features without attached adaptor'); return []; } my $vf_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new( -species => $self->adaptor()->db()->species, -type => "VariationFeature" ); if ($vf_adaptor) { if ( $filter eq 'genotyped' ) { return $vf_adaptor->fetch_all_genotyped_by_Slice($self); } else { return $vf_adaptor->fetch_all_by_Slice($self); } } else { warning( "Variation database must be attached to core database to " . "retrieve variation information" ); return []; } } =head2 get_all_genotyped_VariationFeatures Args : none Description: returns all variation features on this slice that have been genotyped. 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 Caller : contigview, snpview, ldview Status : At Risk : Variation database is under development. =cut sub get_all_genotyped_VariationFeatures { my $self = shift; my $vfa; if ( !$self->adaptor() ) { warning('Cannot get variation features without attached adaptor'); return []; } my $vf_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new( -species => $self->adaptor()->db()->species, -type => "VariationFeature" ); if ($vf_adaptor) { return $vf_adaptor->fetch_all_genotyped_by_Slice($self); } else { warning( "Variation database must be attached to core database to " . "retrieve variation information" ); return []; } } =head2 get_all_DASFeatures 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_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; } =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 @projection; my $current_start = 1; # 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 ); # perform the mapping between this slice and the requested system my @coords; if ( defined $asm_mapper ) { @coords = $asm_mapper->map( $normal_slice->seq_region_name(), $normal_slice->start(), $normal_slice->end(), $normal_slice->strand(), $slice_cs, undef, $to_slice ); } else { $coords[0] = Bio::EnsEMBL::Mapper::Gap->new( $normal_slice->start(), $normal_slice->end() ); } #construct a projection from the mapping results and return it foreach my $coord (@coords) { my $coord_start = $coord->start(); my $coord_end = $coord->end(); my $length = $coord_end - $coord_start + 1; #skip gaps if ( $coord->isa('Bio::EnsEMBL::Mapper::Coordinate') ) { my $coord_cs = $coord->coord_system(); # If the normalised projection just ended up mapping to the # same coordinate system we were already in then we should just # return the original region. This can happen for example, if we # were on a PAR region on Y which refered to X and a projection to # 'toplevel' was requested. # if($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( $coord->id(), $coord_start, $coord_end, $coord->strand() ); my $current_end = $current_start + $length - 1; push @projection, bless( [ $current_start, $current_end, $slice ], "Bio::EnsEMBL::ProjectionSegment" ); } $current_start += $length; } ## end foreach my $coord (@coords) } ## end foreach my $segment (@$normal_slice_proj) # 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; } ## end sub project_to_slice # # 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() . ' ' . $_[0]->seq_region_name(); } =head2 moltype Description: Included for Bio::PrimarySeqI interface compliance (0.7) =cut sub moltype { return 'dna'; } =head2 alphabet Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub alphabet { return 'dna'; } =head2 accession_number Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub accession_number { name(@_); } =head2 is_circular Description: Included for Bio::PrimarySeqI interface compliance (1.2) =cut sub is_circular { my ($self) = @_; if ( !defined( $self->{'circular'} ) ) { my @attrs = grep { $_ } @{ $self->get_all_Attributes('circular_seq') }; $self->{'circular'} = @attrs ? 1 : 0; } return $self->{'circular'}; } 1;