From faa6a31e5576bcbd72e330137835c87c92fe9e5f Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Thu, 27 Sep 2012 14:11:55 +0000
Subject: [PATCH] merge from branch-68
---
.../Bio/EnsEMBL/Utils/ConversionSupport.pm | 24 +++++++++++--------
1 file changed, 14 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index e26dac4393..b499bf3259 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -344,7 +344,7 @@ sub confirm_params {
print "Running script with these parameters:\n\n";
print $self->list_all_params;
- if ($self->param('host') eq 'ensdb-1-10') {
+ if ($self->param('host') eq 'ensdb-web-10') {
# ask user if he wants to proceed
exit unless $self->user_proceed("**************\n\n You're working on ensdb-1-10! Is that correct and you want to continue ?\n\n**************");
}
@@ -367,9 +367,9 @@ sub confirm_params {
sub list_all_params {
my $self = shift;
- my $txt = sprintf " %-21s%-40s\n", qw(PARAMETER VALUE);
- $txt .= " " . "-"x71 . "\n";
- $Text::Wrap::colums = 72;
+ my $txt = sprintf " %-21s%-90s\n", qw(PARAMETER VALUE);
+ $txt .= " " . "-"x121 . "\n";
+ $Text::Wrap::colums = 130;
my @params = $self->allowed_params;
foreach my $key (@params) {
my @vals = $self->param($key);
@@ -994,18 +994,19 @@ sub get_taxonomy_id {
sub get_species_scientific_name {
my ($self, $dba) = @_;
$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 = "SELECT meta_value FROM meta WHERE meta_key = \'species.scientific_name\'";
my $sth = $dba->dbc->db_handle->prepare($sql);
$sth->execute;
my @sp;
while (my @row = $sth->fetchrow_array) {
push @sp, $row[0];
}
+ if (! @sp || @sp > 1) {
+ $self->throw("Could not retrieve a single species scientific name from database.");
+ }
$sth->finish;
- my $species = join(" ", reverse @sp);
- $self->throw("Could not determine species scientific name from database.")
- unless $species;
+ my $species = $sp[0];
+ $species =~ s/ /_/g;
return $species;
}
@@ -1142,6 +1143,9 @@ sub split_chromosomes_by_size {
$top_slices = $slice_adaptor->fetch_all('chromosome',$cs_version,$include_non_reference,$dup);
}
+ # filter out patches, if present
+ $top_slices = [ grep { $_->is_reference or $self->is_haplotype($_,$self->dba) } @$top_slices ];
+
my ($big_chr, $small_chr, $min_big_chr, $min_small_chr);
foreach my $slice (@{ $top_slices }) {
next if ($slice->length eq 10000); #hack for chrY pseudoslice
@@ -1718,7 +1722,7 @@ sub get_unique_genes {
if ( ! $slice->is_reference() and ! $self->is_haplotype($slice,$dba) ) {
# if ( 0 ) {
$patch = 1;
- my $slices = $sa->fetch_by_region_unique( $slice->coord_system_name(),$slice->seq_region_name() );
+ my $slices = $sa->fetch_by_region_unique( $slice->coord_system_name(),$slice->seq_region_name(),undef,undef,undef,$slice->coord_system()->version() );
foreach my $slice ( @{$slices} ) {
push @$genes,@{$ga->fetch_all_by_Slice($slice)};
# my $start = $slice->start;
--
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