Mercurial > repos > dereeper > roary_plots
view Roary/lib/Bio/Roary/AssemblyStatistics.pm @ 0:c47a5f61bc9f draft
Uploaded
author | dereeper |
---|---|
date | Fri, 14 May 2021 20:27:06 +0000 |
parents | |
children |
line wrap: on
line source
package Bio::Roary::AssemblyStatistics; # ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics =head1 SYNOPSIS Given a spreadsheet of gene presence and absence calculate some statistics =cut use Moose; use Bio::Roary::ExtractCoreGenesFromSpreadsheet; use Log::Log4perl qw(:easy); with 'Bio::Roary::SpreadsheetRole'; has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'assembly_statistics.csv' ); has 'job_runner' => ( is => 'ro', isa => 'Str', default => 'Local' ); has 'cpus' => ( is => 'ro', isa => 'Int', default => 1 ); has 'core_definition' => ( is => 'rw', isa => 'Num', default => 0.99 ); has '_cloud_percentage' => ( is => 'rw', isa => 'Num', default => 0.15 ); has '_shell_percentage' => ( is => 'rw', isa => 'Num', default => 0.95 ); has '_soft_core_percentage' => ( is => 'rw', isa => 'Num', default => 0.99 ); has 'verbose' => ( is => 'ro', isa => 'Bool', default => 0 ); has 'contiguous_window' => ( is => 'ro', isa => 'Int', default => 10 ); has 'ordered_genes' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build_ordered_genes' ); has '_genes_to_rows' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__genes_to_rows' ); has 'all_sample_statistics' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build_all_sample_statistics' ); has 'sample_names_to_column_index' => ( is => 'rw', isa => 'Maybe[HashRef]' ); has 'summary_output_filename'=> ( is => 'ro', isa => 'Str', default => 'summary_statistics.txt' ); has 'logger' => ( is => 'ro', lazy => 1, builder => '_build_logger'); has 'gene_category_count' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build_gene_category_count' ); sub BUILD { my ($self) = @_; $self->_genes_to_rows; $self->gene_category_count; } sub _build_logger { my ($self) = @_; Log::Log4perl->easy_init( $ERROR ); my $logger = get_logger(); return $logger; } sub create_summary_output { my ($self) = @_; open(my $fh, '>', $self->summary_output_filename) or Bio::Roary::Exceptions::CouldntWriteToFile->throw(error => "Couldnt write to ".$self->summary_output_filename); my $core_percentage = $self->core_definition()*100; my $soft_core_percentage = $self->_soft_core_percentage*100; my $shell_percentage = $self->_shell_percentage()*100; my $cloud_percentage = $self->_cloud_percentage()*100; my $core_genes = ($self->gene_category_count->{core} ? $self->gene_category_count->{core} : 0); my $soft_core_genes = ($self->gene_category_count->{soft_core} ? $self->gene_category_count->{soft_core} : 0); my $shell_genes =($self->gene_category_count->{shell} ? $self->gene_category_count->{shell} : 0); my $cloud_genes = ($self->gene_category_count->{cloud} ? $self->gene_category_count->{cloud} : 0); my $total_genes = $core_genes + $soft_core_genes + $shell_genes + $cloud_genes ; $self->logger->warn("Very few core genes detected with the current settings. Try modifying the core definition ( -cd 90 ) and/or the blast identity (-i 70) parameters. Also try checking for contamination (-qc) and ensure you only have one species.") if($core_genes < 100); print {$fh} "Core genes\t($core_percentage".'% <= strains <= 100%)'."\t$core_genes\n"; print {$fh} "Soft core genes\t(".$shell_percentage."% <= strains < ".$soft_core_percentage."%)\t$soft_core_genes\n"; print {$fh} "Shell genes\t(".$cloud_percentage."% <= strains < ".$shell_percentage."%)\t$shell_genes\n"; print {$fh} "Cloud genes\t(0% <= strains < ".$cloud_percentage."%)\t$cloud_genes\n"; print {$fh} "Total genes\t(0% <= strains <= 100%)\t$total_genes\n"; close($fh); return 1; } sub _build_gene_category_count { my ($self) = @_; my %gene_category_count; $self->_soft_core_percentage($self->core_definition); if ( $self->_soft_core_percentage <= $self->_shell_percentage ) { $self->_shell_percentage( $self->_soft_core_percentage - 0.01 ); } my $number_of_samples = keys %{ $self->sample_names_to_column_index }; for my $gene_name ( keys %{ $self->_genes_to_rows } ) { my $isolates_with_gene = 0; for ( my $i = $self->_num_fixed_headers ; $i < @{ $self->_genes_to_rows->{$gene_name} } ; $i++ ) { $isolates_with_gene++ if ( defined( $self->_genes_to_rows->{$gene_name}->[$i] ) && $self->_genes_to_rows->{$gene_name}->[$i] ne "" ); } if ( $isolates_with_gene < $self->_cloud_percentage() * $number_of_samples ) { $gene_category_count{cloud}++; } elsif ( $isolates_with_gene < $self->_shell_percentage() * $number_of_samples ) { $gene_category_count{shell}++; } elsif ( $isolates_with_gene < $self->_soft_core_percentage() * $number_of_samples ) { $gene_category_count{soft_core}++; } else { $gene_category_count{core}++; } } return \%gene_category_count; } sub _build_ordered_genes { my ($self) = @_; return Bio::Roary::ExtractCoreGenesFromSpreadsheet->new( spreadsheet => $self->spreadsheet, core_definition => $self->core_definition ) ->ordered_core_genes(); } sub _build__genes_to_rows { my ($self) = @_; my %genes_to_rows; seek( $self->_input_spreadsheet_fh, 0, 0 ); my $header_row = $self->_csv_parser->getline( $self->_input_spreadsheet_fh ); $self->_populate_sample_names_to_column_index($header_row); while ( my $row = $self->_csv_parser->getline( $self->_input_spreadsheet_fh ) ) { next if ( !defined( $row->[0] ) || $row->[0] eq "" ); $genes_to_rows{ $row->[0] } = $row; } return \%genes_to_rows; } sub _populate_sample_names_to_column_index { my ( $self, $row ) = @_; my %samples_to_index; for ( my $i = $self->_num_fixed_headers ; $i < @{$row} ; $i++ ) { next if ( ( !defined( $row->[$i] ) ) || $row->[$i] eq "" ); $samples_to_index{ $row->[$i] } = $i; } $self->sample_names_to_column_index( \%samples_to_index ); } sub _build_all_sample_statistics { my ($self) = @_; my %sample_stats; # For each sample - loop over genes in order - number of contiguous blocks - max size of contiguous block - n50 - incorrect joins for my $sample_name ( sort keys %{ $self->sample_names_to_column_index } ) { $sample_stats{$sample_name} = $self->_sample_statistics($sample_name); } return \%sample_stats; } sub _sample_statistics { my ( $self, $sample_name ) = @_; my $sample_column_index = $self->sample_names_to_column_index->{$sample_name}; my @gene_ids; for my $gene_name ( @{ $self->ordered_genes } ) { my $sample_gene_id = $self->_genes_to_rows->{$gene_name}->[$sample_column_index]; next unless ( defined($sample_gene_id) ); if ( $sample_gene_id =~ /_([\d]+)$/ ) { my $gene_number = $1; push( @gene_ids, $gene_number ); } else { next; } } return $self->_number_of_contiguous_blocks( \@gene_ids ); } sub _number_of_contiguous_blocks { my ( $self, $gene_ids ) = @_; my $current_gene_id = $gene_ids->[0]; my $number_of_blocks = 1; my $largest_block_size = 0; my $block_size = 0; for my $gene_id ( @{$gene_ids} ) { if ( !( ( $current_gene_id + $self->contiguous_window >= $gene_id ) && ( $current_gene_id - $self->contiguous_window <= $gene_id ) ) ) { if ( $block_size >= $largest_block_size ) { $largest_block_size = $block_size; $block_size = 0; } $number_of_blocks++; } $current_gene_id = $gene_id; $block_size++; } if ( $block_size > $largest_block_size ) { $largest_block_size = $block_size; } return { num_blocks => $number_of_blocks, largest_block_size => $largest_block_size }; } no Moose; __PACKAGE__->meta->make_immutable; 1;