Commit b4cb20ed authored by Steve Trevanion's avatar Steve Trevanion
Browse files

merge from branch-vega-49

parent 854b2361
......@@ -60,21 +60,19 @@ sub find_non_overlaps {
=head2 check_remarks_and_update names
Arg[1] : B::E::Gene (with potentially duplicated transcript names)
Arg[2] : FH (for storing list of previous seen genes)
Arg[3] : counter 1 (no. of patched genes)
Arg[4] : counter 2 (no. of patched transcripts)
Example : $support->update_names($gene,$fh,\$c1,\$c2)
Arg[2] : counter 1 (no. of patched genes)
Arg[3] : counter 2 (no. of patched transcripts)
Example : $support->update_names($gene,\$c1,\$c2)
Description: - checks remarks and patches transcripts with identical names according to
CDS and length if there are no fragmented gene/transcript_remarks
- adds remark attribute to gene
- writes IDs of previously seen genes to file
Returntype : true | false (depending on whether patched or not), counter1, counter2
=cut
sub check_remarks_and_update_names {
my $self = shift;
my ($gene,$k_flist_fh,$gene_c,$trans_c) = @_;
my ($gene,$gene_c,$trans_c) = @_;
my $action = ($self->param('dry_run')) ? 'Would add' : 'Added';
my $aa = $gene->adaptor->db->get_AttributeAdaptor;
my $dbh = $gene->adaptor->db->dbc->db_handle;
......@@ -130,7 +128,6 @@ sub check_remarks_and_update_names {
#log if it's been reported before since the gene should have a remark.
elsif ($seen_genes->{$gsi} eq 'fragmented') {
$self->log_warning("PREVIOUS: $action correctly formatted fragmented loci annotation remark for gene $gsi (has previously been OKeyed by Havana as being fragmented but has no Annotation remark, please add one!)\n");
print $k_flist_fh "$gsi\n";
#add gene_attrib anyway.
if (! $self->param('dry_run') ) {
$aa->store_on_Gene($gid,$attrib);
......@@ -241,7 +238,7 @@ sub check_names_and_overlap {
print $n_flist_fh "$gsi\n";
}
#...otherwise if the transcripts do overlap
elsif ($self->param('verbose')) {
else {
$self->log_warning("NEW: Overlapping: $gsi ($g_name) has overlapping transcripts ($all_t_names) with Vega duplicated names and it has no \'Annotation_remark- fragmented_loci\' on the gene or \'\%fragmen\%\' remark on any transcripts. Neither has it been OKeyed by Havana before. Transcript names are being patched but this could be checked by Havana if they were feeling keen.\n");
print $n_flist_fh "$gsi\n";
}
......@@ -300,6 +297,7 @@ OTTHUMG00000058101 = fragmented
OTTHUMG00000150119 = OK
OTTHUMG00000149850 = OK
OTTHUMG00000058101 = OK
OTTHUMG00000058907 = OK
OTTMUSG00000011654 = fragmented
OTTMUSG00000019369 = fragmented
......
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