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Commit d0949712 authored by Eugene Kulesha's avatar Eugene Kulesha
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use db display name + remove synonim duplicates

parent 35f01da3
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Showing with 9 additions and 3 deletions
misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
View file @ d0949712
......@@ -423,8 +423,14 @@ g.seq_region_id=ae.seq_region_id and ae.exc_type='HAP'", [qw(gene_id)]
$xrefs{$type}{ $_->[0] }{ $_->[3] }{ $_->[1] } = 1 if $_->[1];
$xrefs{$type}{ $_->[0] }{ $_->[3] }{ $_->[2] } = 1 if $_->[2];
$xrefs{$type}{ $_->[0] }{ $_->[3] . "_synonym" }{ $_->[4] } = 1
if $_->[4];
## remove the duplicates + Temp fix for metazoa data
if (my $syn = $_->[4]) {
$syn =~ s/^\'|\'$//g;
next if ($syn =~ /^(FBtr|FBpp)\d+/);
next if ($syn =~ /^CG\d+\-/);
$xrefs{$type}{ $_->[0] }{ $_->[3] . "_synonym" }{ $syn } = 1;
}
##
$xrefs_desc{$type}{ $_->[0] }{ $_->[5] } = 1 if $_->[5];
}
......@@ -461,7 +467,7 @@ g.seq_region_id=ae.seq_region_id and ae.exc_type='HAP'", [qw(gene_id)]
my $gene_info = $dbh->selectall_arrayref( "
select gsi.gene_id, tsi.transcript_id, trsi.translation_id,
gsi.stable_id as gsid, tsi.stable_id as tsid, trsi.stable_id as trsid,
g.description, ed.db_name, x.dbprimary_acc,x.display_label, ad.display_label, ad.description, g.source, g.status, g.biotype
g.description, ed.db_display_name, x.dbprimary_acc,x.display_label, ad.display_label, ad.description, g.source, g.status, g.biotype
from (((( $DBNAME.gene_stable_id as gsi, $DBNAME.gene as g,
$DBNAME.transcript_stable_id as tsi,
$DBNAME.analysis_description as ad,
......
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