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Commit 9e66579d authored by Will Spooner's avatar Will Spooner
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Replaced deprecated ens_genomic_align calls, and also changed genomic_hit...

Replaced deprecated ens_genomic_align calls, and also changed genomic_hit seqname to seq_region_name as more reliable
parent c8a67e77
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......@@ -571,11 +571,11 @@ sub store_hsp{
#my $ticket = $hsp->group_ticket || warn( "HSP $id has no ticket" );
my $ticket = $self->ticket || warn( "HSP $id BlastAdaptor has no ticket" );
my $chr_name = 'NULL';
my $chr_start = 'NULL';
my $chr_end = 'NULL';
my $chr_name = '';
my $chr_start = 0;
my $chr_end = 0;
if( my $genomic = $hsp->genomic_hit ){
$chr_name = $genomic->seqname;
$chr_name = $genomic->seq_region_name;
$chr_start = $genomic->start;
$chr_end = $genomic->end;
}
......@@ -710,7 +710,6 @@ AND chr_end >= ? );
push @binded, $chr_end, $chr_start;
}
}
my $sth = $self->db->db_handle->prepare($q);
my $rv = $sth->execute( @binded ) || $self->throw( $sth->errstr );
......@@ -749,11 +748,11 @@ sub get_all_SearchFeatures {
$self->dynamic_use( ref($hsps->[0] ) );
my @feats = ();
foreach my $hsp( @$hsps ){
my $base_align = $hsp->ens_genomic_align || next;
my $base_align = $hsp->genomic_hit || next;
( $ticket ) = split( "!!", $ticket );
my $hsp_id = join( "!!", $ticket, $hsp->token );
$base_align->hseqname( join( ":", $base_align->hseqname, $hsp_id ) );
push @feats, $base_align;
}
......
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