Raw content of Bio::EnsEMBL::Analysis::Tools::MiniSeq
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# Spangle version of the ensembl Transcript object
# POD documentation - main docs before the code
=head1 NAME
MiniSeq - an artificially constructed cDNA on a genomic sequence
=head1 SYNOPSIS
This module is used when we only want to run an analysis over
a part or multiple parts of a sequence.
=head1 DESCRIPTION
Contains details of coordinates of all exons that make
up a gene transcript.
Creation:
my $mini = new Bio::EnsEMBL::Analysis::Tools::MiniSeq(-id => $id,
-pairaln => $pairaln);
$pairaln is a Bio::EnsEMBL::Analysis::PairAlign object containing
one or more feature pairs that represent the mapping of
the genomic coords to the cDNA coords
Manipulation:
my $align = $mini->get_PairAlign;
my $cdnaseq = $mini->get_cDNA_sequence;
# We now do some analysis on the cdnaseq that puts sequence
# features on it. We don't want the coordsin the cDNA frame so
# we now pass them back to the miniseq to convert them into
# genomic coordinates.
my @newfeatures = $mini->convert_FeaturePairs(@featurepairs);
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Analysis::Tools::MiniSeq;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Analysis::Tools::PairAlign;
use Bio::PrimarySeq;
use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump verbose);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw();
sub new {
my($class,@args) = @_;
my $self = {};
bless $self, $class;
my ($id,$pairalign) = rearrange([qw(ID PAIRALIGN)],@args);
verbose('warning');
#No defaults
$self->id($id);
$self->pairAlign($pairalign);
throw("No input id for MiniSeq") unless($self->id);
throw("No input pairalign for MiniSeq") unless($self->pairAlign);
return $self;
}
=head2 id
Title : id
Usage : $obj->id($newval)
Function:
Returns : value of id
Args : newvalue (optional)
=cut
sub id {
my ($self,$arg) = @_;
if(defined($arg)) {
$self->{'_id'} = $arg;
}
return $self->{'_id'};
}
=head2 pairAlign
Title : pairAlign
Usage : $self->pairAlign($pair)
Function: Get/set method for the pairalign object
that stores the cDNA-genomic exon mapping
Returns : Bio::EnsEMBL::Analysis::PairAlign
Args :
=cut
sub pairAlign {
my ($self,$pair) = @_;
if ($pair) {
if( ! $pair->isa("Bio::EnsEMBL::Analysis::Tools::PairAlign") ) {
throw("$pair is not a Bio::EnsEMBL::Analysis::Tools::PairAlign!");
}
foreach my $p (@{$pair->eachFeaturePair}) {
if ($p->strand != 1) {
throw("Can't have a PairAlign object where the strand of the first ".
"object is reversed");
}
}
$self->{'_pair'} = $pair;
}
return $self->{'_pair'};
}
=head2 get_cDNA_sequence
Title : get_cDNA_sequence
Usage : my $seq = $self->get_cDNA_sequence
Function: Returns the cdna sequence corresponding
to the cDNA in the pairAlign object
Example :
Returns : Bio::PrimarySeq
Args : none
=cut
sub get_cDNA_sequence {
my ($self) = @_;
my $seqstr = "";
my @exons = @{$self->pairAlign->eachFeaturePair};
return unless (scalar @exons > 0);
foreach my $exon (@exons) {
$seqstr .= $exon->seq;
}
return new Bio::PrimarySeq('-id' => "genomic" ,
-seq => $seqstr);
}
=head2 convert_FeaturePair
Title : convert_FeaturePair
Usage : my @newfeatures = $self->convert_FeaturePairs($feature)
Function: Converts feature pair coordinates on the cDNA sequence
into an array of feature pairs on the genomic sequence
Example :
Returns : Bio::EnsEMBL::FeaturePair
Args : Array of Bio::EnsEMBL::FeaturePair
=cut
sub convert_FeaturePair {
my ($self,$feature) = @_;
my @newfeatures;
my @tmp = @{$self->pairAlign->convert_FeaturePair($feature)};
push(@newfeatures,@tmp);
return \@newfeatures;
}
=head2 convert_SeqFeature
Title : convert_FeaturePair
Usage : my @newfeatures = $self->convert_FeaturePairs($feature)
Function: Converts feature coordinates on the cDNA sequence
into an array of features on the genomic sequence
Example :
Returns : Bio::EnsEMBL::FeaturePair
Args : Array of Bio::EnsEMBL::FeaturePair
=cut
sub convert_SeqFeature {
my ($self,$feature) = @_;
my @newfeatures;
my @tmp = @{$self->pairAlign->convert_cDNA_feature($feature)};
push(@newfeatures,@tmp);
return \@newfeatures;
}
=head2 convert_PepFeaturePair
Title : convert_PepFeaturePair
Usage : my @newfeatures = $self->convert_PepFeaturePair($feature)
Function: Converts feature pair coordinates on the cDNA sequence
into an array of feature pairs on the genomic sequence
Peptide coordinates are maintained.
Example :
Returns : Array of Bio::EnsEMBL::FeaturePair
Args : Bio::EnsEMBL::FeaturePair
=cut
sub convert_PepFeaturePair {
my ($self,$feature) = @_;
my @newfeatures;
my @tmp = @{$self->pairAlign->convert_FeaturePair($feature)};
# replace protein coordinates
$tmp[0]->hstart($feature->hstart);
$tmp[0]->hend($feature->hend);
# SMJS strand of peptide should be positive?
$tmp[0]->hstrand(1);
push(@newfeatures,@tmp);
return \@newfeatures;
}
1;
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