Unverified Commit 66994335 authored by Marek Szuba's avatar Marek Szuba Committed by GitHub
Browse files

Merge pull request #378 from Ensembl/feature/stop_codon_readthrough_edit

Changed attribute code length to 14 characters.
parents 64549dcc b7521c6f
...@@ -57,7 +57,7 @@ limitations under the License. ...@@ -57,7 +57,7 @@ limitations under the License.
It is believed the STOP codon is instead read as a 'sense' codon, i.e. encodes for an amino acid. It is believed the STOP codon is instead read as a 'sense' codon, i.e. encodes for an amino acid.
The location of a STOP codon readthrough is indicated by an asterisk (*) in the post translation sequence. The location of a STOP codon readthrough is indicated by an asterisk (*) in the post translation sequence.
This class edits the sequence to replace the asterisk (*) with an 'X' to make it similar to Uniprot representation. This class edits the sequence to replace the asterisk (*) with an 'X' to make it similar to RefSeq representation.
=head1 METHODS =head1 METHODS
...@@ -92,7 +92,7 @@ sub new { ...@@ -92,7 +92,7 @@ sub new {
-START => $position, -START => $position,
-END => $position, -END => $position,
-ALT_SEQ => 'X', -ALT_SEQ => 'X',
-CODE => '_stop_codon_readthrough'); -CODE => '_stop_codon_rt');
return $stop_codon_rt_edit; return $stop_codon_rt_edit;
......
...@@ -1108,7 +1108,7 @@ sub get_all_SeqEdits { ...@@ -1108,7 +1108,7 @@ sub get_all_SeqEdits {
my $attribs; my $attribs;
$edits ||= ['initial_met', '_selenocysteine', 'amino_acid_sub', '_stop_codon_readthrough']; $edits ||= ['initial_met', '_selenocysteine', 'amino_acid_sub', '_stop_codon_rt'];
foreach my $edit(@{wrap_array($edits)}){ foreach my $edit(@{wrap_array($edits)}){
...@@ -1149,7 +1149,7 @@ sub get_all_selenocysteine_SeqEdits { ...@@ -1149,7 +1149,7 @@ sub get_all_selenocysteine_SeqEdits {
sub get_all_stop_codon_SeqEdits { sub get_all_stop_codon_SeqEdits {
my ($self) = @_; my ($self) = @_;
return $self->get_all_SeqEdits(['_stop_codon_readthrough']); return $self->get_all_SeqEdits(['_stop_codon_rt']);
} }
=head2 modify_translation =head2 modify_translation
......
...@@ -20,4 +20,4 @@ ...@@ -20,4 +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 23 _stop_codon_rt Stop Codon Readthrough \N
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment