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Commit 592395b1 authored by Dan Staines's avatar Dan Staines
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reformatted to use new perltidy options

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modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
+ 77
− 94
View file @ 592395b1
......@@ -10,12 +10,11 @@ use Bio::EnsEMBL::Utils::ConversionSupport;
use Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::DensityFeature;
## Default run method
## For a given species, generates the required density features in the core database
sub run {
my ($self) = @_;
my $species = $self->param('species');
my $species = $self->param('species');
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');
my $logic_name = $self->param('logic_name');
my $helper = $dba->dbc()->sql_helper();
......@@ -30,73 +29,65 @@ sub run {
Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'DensityType')->store($density_type);
my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice')->fetch_all('toplevel');
my $option = $self->get_option();
my $total = $self->get_total($option);
my $count = 0;
my $total = $self->get_total($option);
my $count = 0;
my @features;
my $iteration = 0;
my @sorted_slices =
sort( { $a->coord_system()->rank() <=> $b->coord_system()->rank()
|| $b->seq_region_length() <=> $a->seq_region_length() } @$slices) ;
my @sorted_slices =
sort({$a->coord_system()->rank() <=> $b->coord_system()->rank() || $b->seq_region_length() <=> $a->seq_region_length()} @$slices);
while (my $slice = shift @sorted_slices) {
$iteration++;
$count += $self->get_density($slice, $option);
if ($slice->has_karyotype) {
my @blocks = $self->generate_blocks($slice);
for my $block (@blocks) {
my $feature = $self->get_density($block, $option);
my $df = Bio::EnsEMBL::DensityFeature->new( -seq_region => $slice,
-start => $block->start - $slice->start + 1,
-end => $block->end - $slice->start + 1,
-density_type => $density_type,
-density_value => $feature);
if ($feature > 0) {
push(@features, $df);
}
}
} else {
my $feature = $self->get_density($slice, $option);
my $df = Bio::EnsEMBL::DensityFeature->new( -seq_region => $slice,
-start => $slice->start,
-end => $slice->end,
-density_type => $density_type,
-density_value => $feature);
if ($feature > 0) {
push(@features, $df);
}
}
if ($count >= $total || $iteration == $max_run) {
last;
}
}
$iteration++;
$count += $self->get_density($slice, $option);
if ($slice->has_karyotype) {
my @blocks = $self->generate_blocks($slice);
for my $block (@blocks) {
my $feature = $self->get_density($block, $option);
my $df = Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
-start => $block->start - $slice->start + 1,
-end => $block->end - $slice->start + 1,
-density_type => $density_type,
-density_value => $feature);
if ($feature > 0) {
push(@features, $df);
}
}
} else {
my $feature = $self->get_density($slice, $option);
my $df = Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
-start => $slice->start,
-end => $slice->end,
-density_type => $density_type,
-density_value => $feature);
if ($feature > 0) {
push(@features, $df);
}
}
if ($count >= $total || $iteration == $max_run) {
last;
}
} ## end while (my $slice = shift ...)
$dfa->store(@features);
}
} ## end sub run
## Creating density type for fixed number of blocks
sub get_density_type {
my ($self, $analysis) = @_;
my $density_type = Bio::EnsEMBL::DensityType->new(
-analysis => $analysis,
-region_features => $self->param('bin_count'),
-value_type => $self->param('value_type')
);
my $density_type = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
-region_features => $self->param('bin_count'),
-value_type => $self->param('value_type'));
return $density_type;
}
## Creating density type for a fixed block size
sub get_density_type_block {
my ($self, $analysis) = @_;
my $density_type = Bio::EnsEMBL::DensityType->new(
-analysis => $analysis,
-block_size => $self->param('block_size'),
-value_type => $self->param('value_type')
);
my $density_type = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
-block_size => $self->param('block_size'),
-value_type => $self->param('value_type'));
return $density_type;
}
## Generates a fixed number of blocks for a given slice
sub generate_blocks {
my ($self, $slice) = @_;
......@@ -104,39 +95,37 @@ sub generate_blocks {
my ($current_end, $current_start, @blocks);
for (my $i = 0; $i < $self->param('bin_count'); $i++) {
$current_start = int($block_size * $i + 1);
$current_end = int($block_size * ($i + 1));
if ($current_end > $slice->end()) {
$current_end = $slice->end();
}
push(@blocks, $slice->sub_Slice($current_start, $current_end));
$current_start = int($block_size*$i + 1);
$current_end = int($block_size*($i + 1));
if ($current_end > $slice->end()) {
$current_end = $slice->end();
}
push(@blocks, $slice->sub_Slice($current_start, $current_end));
}
return @blocks;
}
## Generates blocks of fixed size for a given slice
sub generate_blocks_fixed {
my ($self, $slice) = @_;
my $nb_block = $slice->length()/$self->param('block_size');;
my $nb_block = $slice->length()/$self->param('block_size');
my ($current_end, $current_start, @blocks);
for (my $i = 0; $i < $nb_block; $i++) {
$current_start = int($self->param('block_size') * $i + 1);
$current_end = int($self->param('block_size') * ($i + 1));
if ($current_end > $slice->end()) {
$current_end = $slice->end();
}
push(@blocks, $slice->sub_Slice($current_start, $current_end));
$current_start = int($self->param('block_size')*$i + 1);
$current_end = int($self->param('block_size')*($i + 1));
if ($current_end > $slice->end()) {
$current_end = $slice->end();
}
push(@blocks, $slice->sub_Slice($current_start, $current_end));
}
return @blocks;
}
## Deletes all entries associated to a given analysis
sub delete_old_features {
my ($self, $dba, $logic_name) = @_;
my $helper = $dba->dbc()->sql_helper();
my $sql = q{
my $sql = q{
DELETE df, dt
FROM density_feature df, density_type dt, analysis a, seq_region s, coord_system cs
WHERE df.seq_region_id = s.seq_region_id
......@@ -144,60 +133,56 @@ sub delete_old_features {
AND cs.species_id = ? AND a.analysis_id = dt.analysis_id
AND dt.density_type_id = df.density_type_id
AND a.logic_name = ? };
$helper->execute_update(-SQL => $sql, -PARAMS => [$dba->species_id(), $logic_name]) ;
$helper->execute_update(-SQL => $sql, -PARAMS => [$dba->species_id(), $logic_name]);
}
## Checks if the analysis already exists in the database
## If yes, update the last update date
## If not, add a new analysis entry
sub check_analysis {
my ($self, $dba) = @_;
my $logic_name = $self->param('logic_name');
my $aa = Bio::EnsEMBL::Registry->get_adaptor($self->param('species'), 'core', 'analysis');;
my $analysis = $aa->fetch_by_logic_name($logic_name);
if ( !defined($analysis) ) {
$analysis = $self->get_analysis($logic_name);
$aa->store($analysis);
my $aa = Bio::EnsEMBL::Registry->get_adaptor($self->param('species'), 'core', 'analysis');
my $analysis = $aa->fetch_by_logic_name($logic_name);
if (!defined($analysis)) {
$analysis = $self->get_analysis($logic_name);
$aa->store($analysis);
} else {
my $support = 'Bio::EnsEMBL::Utils::ConversionSupport';
$analysis->created($support->date());
$aa->update($analysis);
my $support = 'Bio::EnsEMBL::Utils::ConversionSupport';
$analysis->created($support->date());
$aa->update($analysis);
}
}
## Creates a new analysis object using the associated information from the production database
sub get_analysis {
my ($self, $logic_name) = @_;
my $prod_dba = $self->get_production_DBAdaptor();
my $helper = $prod_dba->dbc()->sql_helper();
my $sql = q{
my $helper = $prod_dba->dbc()->sql_helper();
my $sql = q{
SELECT distinct display_label, description
FROM analysis_description
WHERE is_current = 1 and logic_name = ? };
my ($display_label, $description) = @{ $helper->execute(-SQL => $sql, -PARAMS => [$logic_name])->[0] } ;
my $analysis = new Bio::EnsEMBL::Analysis(
-logic_name => $logic_name,
-display_label => $display_label,
-description => $description,
-displayable => 1
);
my ($display_label, $description) = @{$helper->execute(-SQL => $sql, -PARAMS => [$logic_name])->[0]};
my $analysis = new Bio::EnsEMBL::Analysis(-logic_name => $logic_name,
-display_label => $display_label,
-description => $description,
-displayable => 1);
return $analysis;
}
sub get_biotype_group {
my ($self, $group) = @_;
my $prod_dba = $self->get_production_DBAdaptor();
my $helper = $prod_dba->dbc()->sql_helper();
my $sql = q{
my $helper = $prod_dba->dbc()->sql_helper();
my $sql = q{
SELECT name
FROM biotype
WHERE object_type = 'gene'
AND is_current = 1
AND biotype_group = ?
AND db_type like '%core%' };
my @biotypes = @{ $helper->execute_simple(-SQL => $sql, -PARAMS => [$group]) };
my @biotypes = @{$helper->execute_simple(-SQL => $sql, -PARAMS => [$group])};
return @biotypes;
}
......@@ -210,7 +195,7 @@ sub get_density {
my ($self, $block, $biotypes) = @_;
my $count = 0;
foreach my $biotype (@$biotypes) {
$count += scalar(@{ $block->get_all_Genes_by_type($biotype) });
$count += scalar(@{$block->get_all_Genes_by_type($biotype)});
}
return $count;
}
......@@ -219,9 +204,7 @@ sub get_total {
my ($self, $option) = @_;
my $species = $self->param('species');
my $ga = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'gene');
return scalar(@{ $ga->fetch_all_by_biotype($option) });
return scalar(@{$ga->fetch_all_by_biotype($option)});
}
1;
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