Mercurial > repos > dereeper > roary_plots
view Roary/lib/Bio/Roary/QC/Report.pm @ 0:c47a5f61bc9f draft
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author | dereeper |
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date | Fri, 14 May 2021 20:27:06 +0000 |
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package Bio::Roary::QC::Report; # ABSTRACT: generate a report based on kraken output =head1 SYNOPSIS =cut use Moose; use File::Temp; use File::Path 'rmtree'; use Cwd; use File::Basename; with 'Bio::Roary::JobRunner::Role'; has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); has 'kraken_exec' => ( is => 'ro', isa => 'Str', default => 'kraken' ); has 'kraken_report_exec' => ( is => 'ro', isa => 'Str', default => 'kraken-report' ); has 'kraken_db' => ( is => 'ro', isa => 'Str', required => 1 ); has 'outfile' => ( is => 'rw', isa => 'Str', default => 'qc_report.csv' ); has '_kraken_data' => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 ); has '_header' => ( is => 'rw', isa => 'Str', lazy_build => 1 ); has 'kraken_memory' => ( is => 'rw', isa => 'Int', default => 2000 ); has '_tmp_directory_obj' => ( is => 'rw', lazy_build => 1 ); has '_tmp_directory' => ( is => 'rw', lazy_build => 1, isa => 'Str', ); sub _nuc_fasta_filename { my ($self, $gff) = @_; my $prefix = basename( $gff, ".gff" ); my $outfile = $self->_tmp_directory . "/$prefix.fna"; return $outfile; } sub _extract_nuc_fasta_cmd { my ($self, $gff) = @_; my $outfile = $self->_nuc_fasta_filename($gff); my $cmd = "sed -n '/##FASTA/,//p' $gff | grep -v \'##FASTA\' > $outfile"; return $cmd; } sub _extract_nuc_files_from_all_gffs { my ($self) = @_; my @nuc_files; my @commands_to_run; for my $input_file(@{$self->input_files}) { push(@nuc_files,$self->_nuc_fasta_filename($input_file)); push(@commands_to_run,$self->_extract_nuc_fasta_cmd($input_file)); } my $kraken_runner_obj = $self->_job_runner_class->new( commands_to_run => \@commands_to_run, memory_in_mb => $self->kraken_memory, verbose => $self->verbose, cpus => $self->cpus ); $kraken_runner_obj->run(); return \@nuc_files; } sub _kraken_cmd { my ( $self, $a, $kraken_output ) = @_; my $kcmd = $self->kraken_exec . " --fasta-input ". " --preload ". " --db " . $self->kraken_db . " --output $kraken_output $a > /dev/null 2>&1"; return $kcmd; } sub _kraken_report_cmd { my ( $self, $k, $report_output ) = @_; my $krcmd = $self->kraken_report_exec . " --db " . $self->kraken_db . " $k > $report_output"; return $krcmd; } sub _kraken_output_filename { my ( $self, $assembly ) = @_; my $kraken_output = $assembly; $kraken_output =~ s/fna$/kraken/; return $kraken_output; } sub _run_kraken_on_nuc_files { my ( $self, $nuc_files ) = @_; my @kraken_output_files; my @commands_to_run; for my $nuc_file(@{$nuc_files}) { my $kraken_output = $self->_kraken_output_filename($nuc_file); push(@kraken_output_files, $kraken_output ); push(@commands_to_run, $self->_kraken_cmd( $nuc_file, $kraken_output )); } my $kraken_runner_obj = $self->_job_runner_class->new( commands_to_run => \@commands_to_run, memory_in_mb => $self->kraken_memory, verbose => $self->verbose, cpus => $self->cpus ); $kraken_runner_obj->run(); for my $filename(@{$nuc_files}) { unlink($filename); } return \@kraken_output_files; } sub _kraken_report_output_filename { my ( $self, $assembly ) = @_; return $assembly.".report"; } sub _run_kraken_report_on_kraken_files { my ( $self, $kraken_files ) = @_; my @kraken_report_output_files; my @commands_to_run; for my $nuc_file(@{$kraken_files}) { my $kraken_output = $self->_kraken_report_output_filename($nuc_file); push(@kraken_report_output_files, $kraken_output ); push(@commands_to_run, $self->_kraken_report_cmd( $nuc_file, $kraken_output )); } my $kraken_runner_obj = $self->_job_runner_class->new( commands_to_run => \@commands_to_run, memory_in_mb => $self->kraken_memory, verbose => $self->verbose, cpus => $self->cpus ); $kraken_runner_obj->run(); for my $filename(@{$kraken_files}) { unlink($filename); } return \@kraken_report_output_files; } sub _build__kraken_data { my $self = shift; my $nuc_files = $self->_extract_nuc_files_from_all_gffs(); my $kraken_files = $self->_run_kraken_on_nuc_files($nuc_files); my $kraken_report_files = $self->_run_kraken_report_on_kraken_files( $kraken_files ); return $self->_parse_kraken_reports($kraken_report_files); } sub _parse_kraken_reports { my ( $self, $kraken_report_files ) = @_; my @report_rows; for my $kraken_report(@{$kraken_report_files}) { push(@report_rows, $self->_parse_kraken_report($kraken_report)); } for my $kraken_report(@{$kraken_report_files}) { unlink($kraken_report); } return \@report_rows; } sub _parse_kraken_report { my ( $self, $kraken_report ) = @_; # parse report open( my $report_fh, '<', $kraken_report ); my $sample_name = $kraken_report; $sample_name =~ s/.report$//; $sample_name =~ s/.kraken$//; my($sample_base_name, $dirs, $suffix) = fileparse($sample_name); my ( $top_genus, $top_species ); while ( <$report_fh> ){ my @parts = split( "\t" ); chomp @parts; $top_genus = $parts[5] if ( (! defined $top_genus) && $parts[3] eq 'G' ); $top_species = $parts[5] if ( (! defined $top_species) && $parts[3] eq 'S' ); last if (defined $top_genus && defined $top_species); } close($report_fh); $top_genus ||= "not_found"; $top_genus =~ s/^\s+//g; $top_species ||= "not_found"; $top_species =~ s/^\s+//g; return [ $sample_base_name, $top_genus, $top_species ]; } sub _build__header { return join( ',', ( 'Sample', 'Genus', 'Species' ) ); } sub _build__tmp_directory_obj { return File::Temp->newdir(DIR => getcwd, CLEANUP => 1 ); } sub _build__tmp_directory { my $self = shift; return $self->_tmp_directory_obj->dirname(); } sub report { my $self = shift; open( OUTFILE, '>', $self->outfile ); print OUTFILE $self->_header . "\n"; for my $line ( @{ $self->_kraken_data } ){ print OUTFILE join( ',', @{ $line } ) . "\n"; } close OUTFILE; } __PACKAGE__->meta->make_immutable; no Moose; 1;