Commit 1c4eec77 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Similar changes as for rev. 1.24 of CoordinateMapper.pm:

  Remove hard-coded external_db_id 11000.

  Change xref.info_type from 'MISC' to 'COORDINATE_OVERLAP'.
parent b81f5332
......@@ -174,14 +174,13 @@ 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'} }
|| 11000, # FIXME ('external_db' needs to be updated)
'accession' => $xref->{'accession'},
'reason' => 'No overlap',
'reason_full' =>
'No coordinate overlap with any Ensembl transcript' };
'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' };
}
$xref_sth->finish();
......@@ -573,17 +572,15 @@ sub dump_xref {
my ($version) = ( $accession =~ /\.(\d+)$/ );
$version ||= 0;
$fh->printf(
"%d\t%d\t%s\t%s\t%d\t%s\t%s\t%s\n",
$xref->{'xref_id'},
$xref->{'external_db_id'},
$accession,
$accession,
$version,
'\N',
'MISC', # FIXME (add new 'info_type' enum 'COORDINATEOVERLAP'
# in release v49)
'\N' # FIXME (possibly)
$fh->printf("%d\t%d\t%s\t%s\t%d\t%s\t%s\t%s\n",
$xref->{'xref_id'},
$xref->{'external_db_id'},
$accession,
$accession,
$version,
'\N',
'COORDINATE_OVERLAP',
'\N' # FIXME (possibly)
);
}
$fh->close();
......
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