Commit 16ae601b authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Having problems with running the coordinate mapping separately, need to

default external_db_id to 11000 ('UCSC') manually.
parent 76e70fcf
......@@ -171,13 +171,14 @@ sub run_coordinatemapping {
while ( my $xref = $xref_sth->fetchrow_hashref() ) {
$unmapped{ $xref->{'coord_xref_id'} } = {
'external_db_id' =>
$XrefMapper::BasicMapper::source_to_external_db_id{ $xref->{
'source_id'} },
'accession' => $xref->{'accession'},
'reason' => 'No overlap',
'reason_full' =>
'No coordinate overlap with any Ensembl transcript' };
'external_db_id' =>
$XrefMapper::BasicMapper::source_to_external_db{ $xref->{
'source_id'} }
|| 11000, # FIXME (11000 is 'UCSC')
'accession' => $xref->{'accession'},
'reason' => 'No overlap',
'reason_full' =>
'No coordinate overlap with any Ensembl transcript' };
}
$xref_sth->finish();
......
......@@ -174,13 +174,14 @@ sub run_coordinatemapping {
while ( my $xref = $xref_sth->fetchrow_hashref() ) {
$unmapped{ $xref->{'coord_xref_id'} } = {
'external_db_id' =>
$XrefMapper::BasicMapper::source_to_external_db_id{ $xref->{
'source_id'} },
'accession' => $xref->{'accession'},
'reason' => 'No overlap',
'reason_full' =>
'No coordinate overlap with any Ensembl transcript' };
'external_db_id' =>
$XrefMapper::BasicMapper::source_to_external_db{ $xref->{
'source_id'} }
|| 11000, # FIXME (11000 is 'UCSC')
'accession' => $xref->{'accession'},
'reason' => 'No overlap',
'reason_full' =>
'No coordinate overlap with any Ensembl transcript' };
}
$xref_sth->finish();
......
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