From 592395b19f6d59fdcf0b7e5fbcf71265601e0cdd Mon Sep 17 00:00:00 2001
From: Dan Staines <dstaines@ebi.ac.uk>
Date: Mon, 5 Nov 2012 10:04:23 +0000
Subject: [PATCH] reformatted to use new perltidy options
---
.../Pipeline/Production/DensityGenerator.pm | 171 ++++++++----------
1 file changed, 77 insertions(+), 94 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm b/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
index 4e87c614ba..fa424456ab 100644
--- a/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
@@ -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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