Commit a0fa8206 authored by Shamika Mohanan's avatar Shamika Mohanan
Browse files

Code updated to implement review comments. New attribute type added to attrib_type table

parent 66f01a20
...@@ -38,7 +38,7 @@ limitations under the License. ...@@ -38,7 +38,7 @@ limitations under the License.
=head1 DESCRIPTION =head1 DESCRIPTION
A representation of a stop codon readthrough edit in a sequence. A representation of a stop codon readthrough edit in a sequence.
=head1 METHODS =head1 METHODS
...@@ -47,15 +47,16 @@ limitations under the License. ...@@ -47,15 +47,16 @@ limitations under the License.
package Bio::EnsEMBL::StopCodonReadthroughEdit; package Bio::EnsEMBL::StopCodonReadthroughEdit;
use strict; use strict;
use warnings;
use parent qw(Bio::EnsEMBL::SeqEdit); use parent qw(Bio::EnsEMBL::SeqEdit);
=head2 new =head2 new
Arg [-START/END] : Arg [-POSITION] :
int - start and end postion of the stop codon readthrough edit in the sequence int - start and end postion of the stop codon readthrough edit in the sequence
Example : $stopcodonrtedit = Bio::EnsEMBL::StopCodonReadthroughEdit->new($coord); Example : $stopcodonrtedit = Bio::EnsEMBL::StopCodonReadthroughEdit->new($posiiton);
Description: Creates a new stop codon readthrough edit object Description: Creates a new stop codon readthrough edit object
Returntype : Bio::EnsEMBL::StopCodonReadthroughEdit Returntype : Bio::EnsEMBL::StopCodonReadthroughEdit
Exceptions : none Exceptions : none
...@@ -65,18 +66,16 @@ use parent qw(Bio::EnsEMBL::SeqEdit); ...@@ -65,18 +66,16 @@ use parent qw(Bio::EnsEMBL::SeqEdit);
=cut =cut
sub new { sub new {
my ($self, $coord) = @_; my ($self, $position) = @_;
my $caller = shift;
my $class = ref($self) || $self;
my $class = ref($caller) || $caller; my $stopcodonrtedit = $class->SUPER::new(
my $self = $class->SUPER::new( -START => $position,
-START => $coord, -END => $position,
-END => $coord,
-ALT_SEQ => 'X', -ALT_SEQ => 'X',
-CODE => '_stop_codon_readthrough', -CODE => '_stop_codon_readthrough');
-NAME => 'Stop Codon Readthrough');
return $self; return $stopcodonrtedit;
} }
......
...@@ -20,3 +20,4 @@ ...@@ -20,3 +20,4 @@
20 proj_parent_g projection parent gene Stable identifier of the parent gene this gene was projected from (projection between different species and/or assemblies). 20 proj_parent_g projection parent gene Stable identifier of the parent gene this gene was projected from (projection between different species and/or assemblies).
21 proj_parent_t projection parent transcript Stable identifier of the parent transcript this transcript was projected from (projection between different species and/or assemblies). 21 proj_parent_t projection parent transcript Stable identifier of the parent transcript this transcript was projected from (projection between different species and/or assemblies).
22 mirna_arm miRNA arm Hairpin arm from which this miRNA has come from 22 mirna_arm miRNA arm Hairpin arm from which this miRNA has come from
23 _stop_codon_readthrough Stop Codon Readthrough \N
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