Commit b197b00b authored by Marek Szuba's avatar Marek Szuba
Browse files

Add the first version of Bio::EnsEMBL::MicroRNA

A minimal extension of Bio::EnsEMBL::RNAProduct, with the only new
information being the arm of the hairpin the miRNA has come from. On the
storage side, this information is stored as a new type of rnaproduct
attribute.
parent 78bc40f3
=head1 LICENSE
Copyright [2018] 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 <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::MicroRNA - A class representing a microRNA product
of a transcript
=head1 DESCRIPTION
TODO
=head1 SYNOPSIS
my $miR = Bio::EnsEMBL::MicroRNA->new(
-SEQ_START => 36,
-SEQ_END => 58
);
# Stable-ID setter
$miR->stable_id('ENSM00090210');
# Get start and end position in the precursor transcript
my $start = $miR->start();
my $end = $miR->end();
=cut
package Bio::EnsEMBL::MicroRNA;
use vars qw($AUTOLOAD);
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw(throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref wrap_array );
use Scalar::Util qw(weaken);
use Bio::EnsEMBL::RNAProduct;
use parent qw(Bio::EnsEMBL::RNAProduct);
=head2 new
Arg [-SEQ_START] : The offset in the Translation indicating the start
position of the product sequence.
Arg [-SEQ_END] : The offset in the Translation indicating the end
position of the product sequence.
Arg [-STABLE_ID] : The stable identifier for this RNAPRoduct
Arg [-VERSION] : The version of the stable identifier
Arg [-DBID] : The internal identifier of this MicroRNA
Arg [-ADAPTOR] : The TranslationAdaptor for this MicroRNA
Arg [-SEQ] : Manually sets the nucleotide sequence of this
rnaproduct. May be useful if this rnaproduct is not
stored in a database.
Arg [-CREATED_DATE] : the date the rnaproduct was created
Arg [-MODIFIED_DATE]: the date the rnaproduct was modified
# FIXME: does all of the above have to be repeated here or can we somehow pull this from the superclass?
Arg: [-ARM] : which arm of the hairpin precursor this miRNA comes
from. Negative values indicate 3', positive ones - 5'.
FIXME: is this right?
Example : my $miR = Bio::EnsEMBL::MicroRNA->new(
-SEQ_START => 36,
-SEQ_END => 58,
-ARM => -1
);
Description: Constructor. Creates a new MicroRNA object
Returntype : Bio::EnsEMBL::MicroRNA
Exceptions : none
Caller : general
Status : In Development
=cut
sub new { ## no critic (Subroutines::RequireArgUnpacking)
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
# FIXME: see the comment about same in RNAProduct::new()
my $type_id = 1;
my ($arm) = rearrange(["ARM"], @_);
$self->{'arm'} = $arm;
return $self;
}
=head2 arm
Example : $mirna_arm = $mirna->arm();
Description : Returns the arm of the hairpin this miRNA comes from.
Negative values indicate the 3' end, positive ones
- the 5' one. FIXME: is this right?
Return type : Integer
Exceptions : warn if multiple 'mirna_arm' attributes exist
Caller : General
Status : Stable
=cut
sub arm {
my ($self, $arm) = @_;
if (defined $arm) {
$self->{'arm'} = $arm;
} elsif (!defined($self->{'arm'})) {
my $arm_attrs = $self->get_all_Attributes('mirna_arm');
my $n_arms = scalar @{$arm_attrs};
if ($n_arms > 0) {
if ($n_arms > 1) {
carp("MicroRNA " . $self->display_id() .
" has multiple arm attributes, using first");
}
$self->{'arm'} = $arm_attrs->[0]->value();
}
}
return $self->{'arm'};
}
=head2 summary_as_hash
Example : $mirna_summary = $mirna->summary_as_hash();
Description : Retrieves a textual summary of this MicroRNA.
Built on top of generic implementation in RNAProduct.
Returns : hashref of arrays of descriptive strings
Status : Intended for internal use
=cut
sub summary_as_hash {
my $self = shift;
my $summary = SUPER::summary_as_hash();
$summary->{'arm'} = $self->arm();
return $summary;
}
1;
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