Raw content of Bio::EnsEMBL::Compara::ConstrainedElement
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Compara::ConstrainedElement
#
# Cared for by Stephen Fitzgerald <ensembl-compara@ebi.ac.uk>
#
# Copyright EMBL-ebi
#
# You may distribute this module under the same terms as perl itself
# pod documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Compara::ConstrainedElement - constrained element data produced by Gerp
=head1 SYNOPSIS
use Bio::EnsEMBL::Compara::ConstrainedElement;
my $constrained_element = new Bio::EnsEMBL::Compara::ConstrainedElement(
-adaptor => $constrained_element_adaptor,
-method_link_species_set_id => $method_link_species_set_id,
-reference_dnafrag_id => $dnafrag_id,
-score => 56.2,
-p_value => '1.203e-6',
-alignment_segments => [ [$dnafrag1_id, $start, $end, $genome_db_id, $dnafrag1_name ], [$dnafrag2_id, ... ], ... ],
-taxonomic_level => "eutherian mammals",
);
GET / SET VALUES
$constrained_element->adaptor($constrained_element_adaptor);
$constrained_element->dbID($constrained_element_id);
$constrained_element->method_link_species_set_id($method_link_species_set_id);
$constrained_element->score(56.2);
$constrained_element->p_value('5.62e-9');
$constrained_element->taxonomic_level("eutherian mammals");
$constrained_element->alignment_segments([ [$dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], ... ]);
$constrained_element->slice($slice);
$constrained_element->start($constrained_element_start - $slice_start + 1);
$constrained_element->end($constrained_element_end - $slice_start + 1);
$constrained_element->reference_dnafrag_id($dnafrag_id);
=head1 OBJECT ATTRIBUTES
=over
=item dbID
corresponds to constrained_element.constrained_element_id
=item adaptor
Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object to access DB
=item method_link_species_set_id
corresponds to method_link_species_set.method_link_species_set_id (external ref.)
=item score
corresponds to constrained_element.score
=item p_value
corresponds to constrained_element.p_value
=item taxonomic_level
corresponds to constrained_element.taxonoic_level
=item slice
corresponds to a Bio::EnsEMBL::Slice
=item start
corresponds to a constrained_element.dnafrag_start (in slice coordinates)
=item end
corresponds to a constrained_element.dnafrag_end (in slice coordinates)
=item $alignment_segments
listref of listrefs (each of which contain 5 strings (dnafrag.dnafrag_id, constrained_element.dnafrag_start,
constrained_element.dnafrag_end, genome_db.genome_db_id, dnafrag.dnafrag_name)
[ [ $dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], .. ]
Each inner listref contains information about one of the species sequences which make up the constarained
element block from the alignment.
=back
=head1 AUTHOR
Stephen Fitzgerald (ensembl-compara@ebi.ac.uk)
=head1 COPYRIGHT
Copyright (c) 2009. EnsEMBL Team
You may distribute this module under the same terms as perl itself
=head1 CONTACT
This modules is part of the EnsEMBL project ()
Questions can be posted to the ensembl-dev mailing list:
ensembl-dev@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Compara::ConstrainedElement;
use strict;
# Object preamble
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning info deprecate verbose);
use Bio::EnsEMBL::Compara::DnaFrag;
use Bio::SimpleAlign;
use Data::Dumper;
=head2 new (CONSTRUCTOR)
Arg [-dbID] : int $dbID (the database ID for
the constrained element block for this object)
Arg [-ADAPTOR]
: (opt.) Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor $adaptor
(the adaptor for connecting to the database)
Arg [-METHOD_LINK_SPECIES_SET_ID]
: int $mlss_id (the database internal ID for the $mlss)
Arg [-SCORE]
: float $score (the score of this alignment)
Arg [-ALIGNMENT_SEGMENTS]
: (opt.) listref of listrefs which each contain 5 values
[ [ $dnafrag_id, $dnafrag_start, $dnafrag_end, $genome_db_id, $dnafrag_name ], ... ]
corresponding to the all the species in the constrained element block.
Arg [-P_VALUE]
: (opt.) string $p_value (the p_value of this constrained element)
Arg [-TAXONOMIC_LEVEL]
: (opt.) string $taxonomic_level (the taxonomic level of the alignments from which the
constrained element was derived)
Arg [-SLICE]
: (opt.) Bio::EnsEMBL::Slice object
Arg [-START]
: (opt.) int ($dnafrag_start - Bio::EnsEMBL::Slice->start + 1).
Arg [-END]
: (opt.) int ($dnafrag_end - Bio::EnsEMBL::Slice->start + 1).
Arg [-REFERENCE_DNAFRAG_ID]
: (opt.) int $dnafrag_id of the slice or dnafrag
Example : my $constrained_element =
new Bio::EnsEMBL::Compara::ConstrainedElement(
-dbID => $constrained_element_id,
-adaptor => $adaptor,
-method_link_species_set_id => $method_link_species_set_id,
-score => 28.2,
-alignment_segments => [ [ $dnafrag_id, $dnafrag_start, $dnafrag_end, $genome_db_id, $dnafrag_name ], .. ],
#danfarg_[start|end|id] from constrained_element table
-p_value => '5.023e-6',
-taxonomic_level => "eutherian mammals",
-slice => $slice_obj,
-start => ( $dnafrag_start - $slice_obj->start + 1),
-end => ( $dnafrag_end - $slice_obj->start + 1),
-reference_dnafrag_id => $dnafrag_id,
);
Description: Creates a new ConstrainedElement object
Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElement
Exceptions : none
Caller : general
=cut
sub new {
my($class, @args) = @_;
my $self = {};
bless $self,$class;
my ($adaptor, $dbID, $alignment_segments,
$method_link_species_set_id, $score, $p_value,
$taxonomic_level, $slice, $start, $end, $reference_dnafrag_id) =
rearrange([qw(
ADAPTOR DBID ALIGNMENT_SEGMENTS
METHOD_LINK_SPECIES_SET_ID SCORE P_VALUE TAXONOMIC_LEVEL
SLICE START END REFERENCE_DNAFRAG_ID
)],
@args);
$self->adaptor($adaptor) if (defined ($adaptor));
$self->dbID($dbID)
if (defined ($dbID));
$self->method_link_species_set_id($method_link_species_set_id)
if (defined ($method_link_species_set_id));
$self->alignment_segments($alignment_segments)
if (defined ($alignment_segments));
$self->score($score) if (defined ($score));
$self->p_value($p_value) if (defined ($p_value));
$self->taxonomic_level($taxonomic_level)
if (defined($taxonomic_level));
$self->slice($slice) if (defined ($slice));
$self->start($start) if (defined ($start));
$self->end($end) if (defined ($end));
$self->reference_dnafrag_id($reference_dnafrag_id)
if (defined($reference_dnafrag_id));
return $self;
}
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
=head2 adaptor
Arg [1] : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor
Example : my $cons_ele_adaptor = $constrained_element->adaptor();
Example : $cons_ele_adaptor->adaptor($cons_ele_adaptor);
Description: Getter/Setter for the adaptor this object uses for database
interaction.
Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object
Exceptions : thrown if $adaptor is not a
Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object
Caller : general
=cut
sub adaptor {
my ($self, $adaptor) = @_;
if (defined($adaptor)) {
throw("$adaptor is not a Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object")
unless ($adaptor->isa("Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor"));
$self->{'adaptor'} = $adaptor;
}
return $self->{'adaptor'};
}
=head2 dbID
Arg [1] : integer $dbID
Example : my $dbID = $constrained_element->dbID();
Example : $constrained_element->dbID(2);
Description: Getter/Setter for the attribute dbID
Returntype : integer
Exceptions : returns undef if no ref.dbID
Caller : general
=cut
sub dbID {
my ($self, $dbID) = @_;
if (defined($dbID)) {
$self->{'dbID'} = $dbID;
}
return $self->{'dbID'};
}
=head2 p_value
Arg [1] : float $p_value
Example : my $p_value = $constrained_element->p_value();
Example : $constrained_element->p_value('5.35242e-105');
Description: Getter/Setter for the attribute p_value
Returntype : float
Exceptions : returns undef if no ref.p_value
Caller : general
=cut
sub p_value {
my ($self, $p_value) = @_;
if (defined($p_value)) {
$self->{'p_value'} = $p_value;
}
return $self->{'p_value'};
}
=head2 taxonomic_level
Arg [1] : string $taxonomic_level
Example : my $taxonomic_level = $constrained_element->taxonomic_level();
Example : $constrained_element->taxonomic_level("eutherian mammals");
Description: Getter/Setter for the attribute taxonomic_level
Returntype : string
Exceptions : returns undef if no ref.taxonomic_level
Caller : general
=cut
sub taxonomic_level {
my ($self, $taxonomic_level) = @_;
if (defined($taxonomic_level)) {
$self->{'taxonomic_level'} = $taxonomic_level;
}
return $self->{'taxonomic_level'};
}
=head2 score
Arg [1] : float $score
Example : my $score = $constrained_element->score();
Example : $constrained_element->score(16.8);
Description: Getter/Setter for the attribute score
Returntype : float
Exceptions : returns undef if no ref.score
Caller : general
=cut
sub score {
my ($self, $score) = @_;
if (defined($score)) {
$self->{'score'} = $score;
}
return $self->{'score'};
}
=head2 method_link_species_set_id
Arg [1] : integer $method_link_species_set_id
Example : $method_link_species_set_id = $constrained_element->method_link_species_set_id;
Example : $constrained_element->method_link_species_set_id(3);
Description: Getter/Setter for the attribute method_link_species_set_id.
Returntype : integer
Exceptions : returns undef if no ref.method_link_species_set_id
Caller : object::methodname
=cut
sub method_link_species_set_id {
my ($self, $method_link_species_set_id) = @_;
if (defined($method_link_species_set_id)) {
$self->{'method_link_species_set_id'} = $method_link_species_set_id;
}
return $self->{'method_link_species_set_id'};
}
=head2 alignment_segments
Arg [1] : listref $alignment_segments [ [ $dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], .. ]
Example : my $alignment_segments = $constrained_element->alignment_segments();
$constrained_element->alignment_segments($alignment_segments);
Description: Getter/Setter for the attribute alignment_segments
Returntype : listref
Exceptions : returns undef if no ref.alignment_segments
Caller : general
=cut
sub alignment_segments {
my ($self, $alignment_segments) = @_;
if (defined($alignment_segments)) {
$self->{'alignment_segments'} = $alignment_segments;
}
return $self->{'alignment_segments'};
}
=head2 slice
Arg [1] : Bio::EnsEMBL::Slice $slice
Example : $slice = $constrained_element->slice;
Example : $constrained_element->slice($slice);
Description: Getter/Setter for the attribute slice.
Returntype : Bio::EnsEMBL::Slice object
Exceptions : returns undef if no ref.slice
Caller : object::methodname
=cut
sub slice {
my ($self, $slice) = @_;
if (defined($slice)) {
$self->{'slice'} = $slice;
}
return $self->{'slice'};
}
=head2 start
Arg [1] : (optional) int $start
Example : $start = $constrained_element->start;
Example : $constrained_element->start($start);
Description: Getter/Setter for the attribute start.
Returntype : int
Exceptions : returns undef if no ref.start
Caller : object::methodname
=cut
sub start {
my ($self, $start) = @_;
if (defined($start)) {
$self->{'start'} = $start;
}
return $self->{'start'};
}
=head2 end
Arg [1] : (optional) int $end
Example : $end = $constrained_element->end;
Example : $constrained_element->end($end);
Description: Getter/Setter for the attribute end.
Returntype : int
Exceptions : returns undef if no ref.end
Caller : object::methodname
=cut
sub end {
my ($self, $end) = @_;
if (defined($end)) {
$self->{'end'} = $end;
}
return $self->{'end'};
}
=head2 reference_dnafrag_id
Arg [1] : (optional) int $reference_dnafrag_id
Example : $dnafrag_id = $constrained_element->reference_dnafrag_id;
Example : $constrained_element->reference_dnafrag_id($dnafrag_id);
Description: Getter/Setter for the attribute end.
Returntype : int
Exceptions : returns undef if no ref.reference_dnafrag_id
Caller : object::methodname
=cut
sub reference_dnafrag_id {
my ($self, $reference_dnafrag_id) = @_;
if (defined($reference_dnafrag_id)) {
$self->{'reference_dnafrag_id'} = $reference_dnafrag_id;
}
return $self->{'reference_dnafrag_id'};
}
=head2 get_SimpleAlign
Arg [1] : The method_link_species_set_object of the original alignment
Example : my $out = Bio::AlignIO->newFh(-fh=>\*STDOUT, -format=> "clustalw");
my$cons = $ce_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $slice);
foreach my $simple_align(@{ $ce->get_SimpleAlign($prev_mlss, "uc") }) {
print $out $simple_align;
}
Note : Where constrained elements occur in overlapping genomic_align_blocks there will be ambiguities
in associating an alignment with the correct constrined_element_id.
Description: Rebuilds the constrained element alignment
Returntype : an arrayref of Bio::SimpleAlign objects
Exceptions : throw if Arg-1 is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
Caller : object::methodname
=cut
sub get_SimpleAlign {
my ($self, $orig_mlss, @flags) = @_;
if (defined($orig_mlss)) {
throw("$orig_mlss is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object")
unless ($orig_mlss->isa("Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
} else {
throw("undefined Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
}
# setting the flags
my $skip_empty_GenomicAligns = 1;
my @SimpleAligns;
my $uc = 0;
my $translated = 0;
for my $flag ( @flags ) {
$uc = 1 if ($flag =~ /^uc$/i);
$translated = 1 if ($flag =~ /^translated$/i);
}
my $genomic_align_block_adaptor = $self->adaptor->db->get_GenomicAlignBlock;
my $gabs = $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(
$orig_mlss, $self->slice->sub_Slice($self->start, $self->end, $self->slice->strand));
foreach my $this_genomic_align_block(@$gabs) {
my $sa = Bio::SimpleAlign->new();
my $bio07 = 0;
if(!$sa->can('add_seq')) {
$bio07 = 1;
}
my $reference_genomic_align = $this_genomic_align_block->reference_genomic_align();
my $restricted_gab = $this_genomic_align_block->restrict_between_reference_positions(
($self->slice->start + $self->start - 1),
($self->slice->start + $self->end - 1),
$reference_genomic_align,
$skip_empty_GenomicAligns);
foreach my $genomic_align( @{ $restricted_gab->get_all_GenomicAligns } ) {
my $alignSeq = $genomic_align->aligned_sequence;
my $loc_seq = Bio::LocatableSeq->new(
-SEQ => $uc ? uc $alignSeq : lc $alignSeq,
-START => $genomic_align->dnafrag_start,
-END => $genomic_align->dnafrag_end,
-ID => $this_genomic_align_block->dbID . "/" .
$genomic_align->dnafrag->genome_db_id . "/" . $genomic_align->dnafrag->name,
-STRAND => $genomic_align->dnafrag_strand);
if($bio07) {
$sa->addSeq($loc_seq);
}else{
$sa->add_seq($loc_seq);
}
}
push(@SimpleAligns, $sa);
}
warn "overlapping constrained elements for ", $self->dbID, "\n" if (@SimpleAligns > 1);
return \@SimpleAligns;
}
1;
]]>