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Commit d657d7a2 authored by Andy Yates's avatar Andy Yates
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Conflict resolved we think. 1.18 code had very odd hash assignment/caching...

Conflict resolved we think. 1.18 code had very odd hash assignment/caching code which should not have worked
parent 58494488
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......@@ -448,50 +448,11 @@ g.seq_region_id=ae.seq_region_id and ae.exc_type='HAP'", [qw(gene_id)]
# $exons{ $_->[0] }{ $_->[1] } = 1;
# }
<<<<<<< ebi_search_dump.pl
my $dbh2 = DBI->connect( "$dsn:$DBNAME", $user, $pass )
or die "DBI::error";
my $gene_info = $dbh2->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,
=======
my %exons = ();
my $get_genes_sth = $dbh->prepare(
"select distinct t.gene_id, e.stable_id
from transcript as t, exon_transcript as et, exon as e
where t.transcript_id = et.transcript_id and et.exon_id = e.exon_id"
);
$get_genes_sth->execute;
my $gene_rows = []; # cache for batches of rows
while (
my $row = (
shift(@$gene_rows) || # get row from cache, or reload cache:
shift(
@{
$gene_rows =
$get_genes_sth->fetchall_arrayref( undef, 10_000 )
|| []
}
)
)
)
{
push @{ $ortholog_lookup->{ $row->[0] } },
[ $row->[1], $orth_species->{ $row->[2] } ];
$exons{ $row->[0] }{ $row->[1] } = 1;
}
my $gene_info = $dbh->selectall_arrayref( "
select g.gene_id, t.transcript_id, tr.translation_id,
g.stable_id as gsid, t.stable_id as tsid, tr.stable_id as trsid,
>>>>>>> 1.18
g.description, ed.db_name, x.dbprimary_acc,x.display_label, ad.display_label, ad.description, g.source, g.status, g.biotype
from ((( $DBNAME.gene as g,
$DBNAME.analysis_description as ad,
......
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