Commit 893438b2 authored by Web Admin's avatar Web Admin
Browse files

Added %age context on Gene based slices, tweaks to stable id fetches, and white space removal

parent 0364683f
......@@ -222,7 +222,14 @@ sub get_translation_archive_id {
my $self = shift;
if( $self->type() eq "Transcript" ) {
return $self->adaptor->fetch_by_transcript_archive_id( $self );
return [$self->adaptor->fetch_by_transcript_archive_id( $self )];
} elsif( $self->type() eq "Gene" ) {
my $transcripts = $self->adaptor->fetch_all_by_gene_archive_id( $self );
my @peptides ;
for (@$transcripts) {
push @peptides , $self->adaptor->fetch_by_transcript_archive_id( $_ );
}
return \@peptides;
} else {
return undef;
}
......
......@@ -468,10 +468,13 @@ sub fetch_by_gene_stable_id{
if( !defined $geneid ) {
$self->throw("Must have gene id to fetch Slice of gene");
}
if( !defined $size ) {$size=0;}
my ($chr_name,$start,$end) = $self->_get_chr_start_end_of_gene($geneid);
if( $size =~/([\d+\.]+)%/ ) {
$size = int($1/100 * ($end-$start+1));
}
if( !defined $size ) {$size=0;}
if( !defined $start ) {
my $type = $self->db->assembly_type()
or $self->throw("No assembly type defined");
......
......@@ -71,8 +71,6 @@ sub new {
return $self;
}
=head2 fetch_all_by_gene_id_list
Arg [1] : arrayref $gene_ids
......
......@@ -895,7 +895,6 @@ sub get_all_peptide_variations {
return \%out;
}
=head2 get_all_SNPs
Arg [1] : (optional) int $flanking
......
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