Commit 24395c71 authored by Steve Trevanion's avatar Steve Trevanion
Browse files

merge from branch-vega-38-dev

parent a794d0fc
......@@ -117,8 +117,10 @@ my $chr_slices = $support->split_chromosomes_by_size(5000000);
# known biotype/status pairs and associated density type
my %gene_types = (
"protein_coding_KNOWN" => "knownPCodDensity",
"protein_coding_in_progress_KNOWN" => "knownPCodDensity",
"processed_transcript_KNOWN" => "knownPTransDensity",
"protein_coding_NOVEL" => "novelPCodDensity",
"protein_coding_in_progress_NOVEL" => "novelPCodDensity",
"processed_transcript_NOVEL" => "novelPTransDensity",
"processed_transcript_PUTATIVE" => "putativePTransDensity",
"protein_coding_PREDICTED" => "predictedPCodDensity",
......
......@@ -251,9 +251,14 @@ sub confirm_params {
print "Running script with these parameters:\n\n";
print $self->list_all_params;
if ($self->param('host') eq 'web-4-11') {
# ask user if he wants to proceed
exit unless $self->user_proceed("**************\n\n You're working on web-4-11! Is that correct and you want to continue ?\n\n**************");
}
else {
# ask user if he wants to proceed
exit unless $self->user_proceed("Continue?");
}
return(1);
}
......@@ -938,15 +943,6 @@ sub get_species_scientific_name {
$dba ||= $self->dba;
my $sql_tmp = "SELECT meta_value FROM meta WHERE meta_key = \'species.classification\' ORDER BY meta_id";
my $sql = $dba->dbc->add_limit_clause($sql_tmp,2);
# my $sql = qq(
# SELECT
# meta_value
# FROM
# meta
# WHERE meta_key = "species.classification"
# ORDER BY meta_id
# LIMIT 2
# );
my $sth = $dba->dbc->db_handle->prepare($sql);
$sth->execute;
my @sp;
......
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