Raw content of Bio::EnsEMBL::Compara::AlignedMember
<![CDATA[=head1 NAME
AlignedMember - DESCRIPTION of Object
=head1 DESCRIPTION
A subclass of Member which extends it to allow it to be aligned with other
AlignedMember objects. General enough to allow for global, local, pair-wise and
multiple alignments. To be used primarily in NestedSet Tree data-structure.
=head1 CONTACT
Contact Jessica Severin on module implemetation/design detail: jessica@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::AlignedMember;
use strict;
#use Time::HiRes qw(time gettimeofday tv_interval);
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Compara::Member;
our @ISA = qw(Bio::EnsEMBL::Compara::Member);
##################################
# overriden superclass methods
##################################
sub copy {
my $self = shift;
my $mycopy = $self->SUPER::copy;
bless $mycopy, "Bio::EnsEMBL::Compara::AlignedMember";
$mycopy->cigar_line($self->cigar_line);
$mycopy->cigar_start($self->cigar_start);
$mycopy->cigar_end($self->cigar_end);
$mycopy->perc_cov($self->perc_cov);
$mycopy->perc_id($self->perc_id);
$mycopy->perc_pos($self->perc_pos);
$mycopy->method_link_species_set_id($self->method_link_species_set_id);
return $mycopy;
}
sub print_node {
my $self = shift;
printf("(%s %d,%d)", $self->node_id, $self->left_index, $self->right_index);
printf(" %s", $self->genome_db->name) if($self->genome_db_id and $self->adaptor);
if($self->gene_member) {
printf(" %s %s %s:%d-%d",
$self->gene_member->stable_id, $self->gene_member->display_label || '', $self->gene_member->chr_name,
$self->gene_member->chr_start, $self->gene_member->chr_end);
} elsif($self->stable_id) {
printf(" (%d) %s", $self->member_id, $self->stable_id);
}
print("\n");
}
#####################################################
sub name {
my $self = shift;
return $self->stable_id(@_);
}
sub cigar_line {
my $self = shift;
$self->{'_cigar_line'} = shift if(@_);
return $self->{'_cigar_line'};
}
sub cigar_start {
my $self = shift;
$self->{'_cigar_start'} = shift if(@_);
return $self->{'_cigar_start'};
}
sub cigar_end {
my $self = shift;
$self->{'_cigar_end'} = shift if(@_);
return $self->{'_cigar_end'};
}
sub perc_cov {
my $self = shift;
$self->{'perc_cov'} = shift if(@_);
return $self->{'perc_cov'};
}
sub perc_id {
my $self = shift;
$self->{'perc_id'} = shift if(@_);
return $self->{'perc_id'};
}
sub perc_pos {
my $self = shift;
$self->{'perc_pos'} = shift if(@_);
return $self->{'perc_pos'};
}
sub method_link_species_set_id {
my $self = shift;
$self->{'method_link_species_set_id'} = shift if(@_);
$self->{'method_link_species_set_id'} = 0 unless(defined($self->{'method_link_species_set_id'}));
return $self->{'method_link_species_set_id'};
}
sub alignment_string {
my $self = shift;
my $exon_cased = shift;
unless (defined $self->cigar_line && $self->cigar_line ne "") {
throw("To get an alignment_string, the cigar_line needs to be define\n");
}
unless (defined $self->{'alignment_string'}) {
my $sequence;
if ($exon_cased) {
$sequence = $self->sequence_exon_cased;
} else {
$sequence = $self->sequence;
}
if (defined $self->cigar_start || defined $self->cigar_end) {
unless (defined $self->cigar_start && defined $self->cigar_end) {
throw("both cigar_start and cigar_end should be defined");
}
my $offset = $self->cigar_start - 1;
my $length = $self->cigar_end - $self->cigar_start + 1;
$sequence = substr($sequence, $offset, $length);
}
my $cigar_line = $self->cigar_line;
$cigar_line =~ s/([MD])/$1 /g;
my @cigar_segments = split " ",$cigar_line;
my $alignment_string = "";
my $seq_start = 0;
foreach my $segment (@cigar_segments) {
if ($segment =~ /^(\d*)D$/) {
my $length = $1;
$length = 1 if ($length eq "");
$alignment_string .= "-" x $length;
} elsif ($segment =~ /^(\d*)M$/) {
my $length = $1;
$length = 1 if ($length eq "");
$alignment_string .= substr($sequence,$seq_start,$length);
$seq_start += $length;
}
}
$self->{'alignment_string'} = $alignment_string;
}
return $self->{'alignment_string'};
}
=head2 cdna_alignment_string
Arg [1] : none
Example : my $cdna_alignment = $aligned_member->cdna_alignment_string();
Description: Converts the peptide alignment string to a cdna alignment
string. This only works for EnsEMBL peptides whose cdna can
be retrieved from the attached EnsEMBL databse.
If the cdna cannot be retrieved undef is returned and a
warning is thrown.
Returntype : string
Exceptions : none
Caller : general
=cut
sub cdna_alignment_string {
my $self = shift;
throw("can't connect to CORE to get transcript and cdna for "
. "genome_db_id:" . $self->genome_db_id )
unless($self->transcript);
unless (defined $self->{'cdna_alignment_string'}) {
my $cdna = $self->transcript->translateable_seq;
if (defined $self->cigar_start || defined $self->cigar_end) {
unless (defined $self->cigar_start && defined $self->cigar_end) {
throw("both cigar_start and cigar_end should be defined");
}
my $offset = $self->cigar_start * 3 - 3;
my $length = ($self->cigar_end - $self->cigar_start + 1) * 3;
$cdna = substr($cdna, $offset, $length);
}
my $cdna_len = length($cdna);
my $start = 0;
my $cdna_align_string = '';
# foreach my $pep (split(//, $self->alignment_string)) { # Speed up below
my $alignment_string = $self->alignment_string;
foreach my $pep (unpack("A1" x length($alignment_string), $alignment_string)) {
if($pep eq '-') {
$cdna_align_string .= '--- ';
} else {
my $codon = substr($cdna, $start, 3);
unless (length($codon) == 3) {
# sometimes the last codon contains only 1 or 2 nucleotides.
# making sure that it has 3 by adding as many Ns as necessary
$codon .= 'N' x (3 - length($codon));
}
$cdna_align_string .= $codon . ' ';
$start += 3;
}
}
$self->{'cdna_alignment_string'} = $cdna_align_string
}
return $self->{'cdna_alignment_string'};
}
#############################################################
#
# orthologue and paralogue searching
#
#############################################################
sub orthologue_in_genome {
my $self = shift;
my $genomedb = shift;
throw("[$genomedb] must be a Bio::EnsEMBL::Compara::GenomeDB object")
unless ($genomedb and $genomedb->isa("Bio::EnsEMBL::Compara::GenomeDB"));
# my $starttime = time();
my $all_leaves = $self->root->get_all_leaves;
foreach my $member (@{$all_leaves}) {
}
# printf("%1.3f secs to find orthologue\n", (time()-$starttime));
}
sub get_leaves_in_genome {
my $self = shift;
}
1;
]]>