Commit 35f46427 authored by Ian Longden's avatar Ian Longden
Browse files

set xref info_type to INFERRED_PAIR for those ones

parent f7899900
......@@ -56,6 +56,7 @@ sub process{
my $ox_get_id_sth = $self->xref->dbc->prepare("select object_xref_id,ox_status from object_xref where xref_id = ? and ensembl_id = ? and ensembl_object_type = ?");
my $ox_update_sth = $self->xref->dbc->prepare('update object_xref set ox_status = "DUMP_OUT", linkage_type = "INFERRED_PAIR" where object_xref_id = ?');
my $xref_update_sth = $self->xref->dbc->prepare('update xref set info_type = "INFERRED_PAIR" where xref_id = ?');
$psth->execute() || die "execute failed";
my ($acc1, $acc2);
......@@ -120,12 +121,14 @@ sub process{
die "Duplicate but can't find the original?? xref_id = $xref_id, ensembl_id = $transcript_id, type = Transcript\n";
}
$ox_update_sth->execute($old_object_xref_id)|| die "Could not set update for object_xref_id = $old_object_xref_id";
$xref_update_sth->execute($xref_id)|| die "Could not set update for xref_id = $xref_id";
}
else{
die "Problem loading error is $err\n";
}
}
else{
$xref_update_sth->execute($xref_id)|| die "Could not set update for xref_id = $xref_id";
$change{"NEW"}++;
}
# print "insert $xref_id transcript $transcript_id ........\n";
......@@ -172,12 +175,14 @@ sub process{
die "Duplicate but can't find the original?? xref_id = $xref_id, ensembl_id = $translation_id, type = Translation\n";
}
$ox_update_sth->execute($old_object_xref_id)|| die "Could not set update for object_xref_id = $old_object_xref_id";
$xref_update_sth->execute($xref_id)|| die "Could not set update for xref_id = $xref_id";
}
else{
die "Problem loading error is $err\n";
}
}
else{
$xref_update_sth->execute($xref_id)|| die "Could not set update for xref_id = $xref_id";
$change{"NEW"}++;
}
# print "insert $xref_id translation $translation_id ........\n";
......@@ -193,6 +198,8 @@ sub process{
$ox_count_sth->finish;
$ox_transcript_sth->finish;
$ox_translation_sth->finish;
$ox_update_sth->finish;
$xref_update_sth->finish;
$xref_sth->finish;
foreach my $key (keys %change){
print "\t$key\t".$change{$key}."\n";
......@@ -200,6 +207,7 @@ sub process{
print "$refseq_count new relationships added\n";
my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('processed_pairs',now())");
$sth_stat->execute();
$sth_stat->finish;
}
1;
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