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Merge pull request #34 from andrewjpage/master
run post analysis as a job
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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env perl | ||
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| package Bio::PanGenome::Main::PanGenomePostAnalysis; | ||
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| # ABSTRACT: Perform the post analysis on the pan genome | ||
| # PODNAME: pan_genome_post_analysis | ||
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| =head1 SYNOPSIS | ||
| Perform the post analysis on the pan genome | ||
| =cut | ||
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| BEGIN { unshift( @INC, '../lib' ) } | ||
| BEGIN { unshift( @INC, './lib' ) } | ||
| BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } | ||
| use Bio::PanGenome::CommandLine::PanGenomePostAnalysis; | ||
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| Bio::PanGenome::CommandLine::PanGenomePostAnalysis->new(args => \@ARGV, script_name => $0)->run; |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,107 @@ | ||
| package Bio::PanGenome::CommandLine::PanGenomePostAnalysis; | ||
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| # ABSTRACT: Perform the post analysis on the pan genome | ||
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| =head1 SYNOPSIS | ||
| Perform the post analysis on the pan genome | ||
| =cut | ||
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| use Moose; | ||
| use Getopt::Long qw(GetOptionsFromArray); | ||
| use Bio::PanGenome::PostAnalysis; | ||
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| has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); | ||
| has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
| has 'help' => ( is => 'rw', isa => 'Bool', default => 0 ); | ||
| has '_error_message' => ( is => 'rw', isa => 'Str' ); | ||
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| has 'fasta_files' => ( is => 'rw', isa => 'ArrayRef' ); | ||
| has 'input_files' => ( is => 'rw', isa => 'ArrayRef'); | ||
| has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' ); | ||
| has 'output_pan_geneome_filename' => ( is => 'rw', isa => 'Str', default => 'pan_genome.fa' ); | ||
| has 'output_statistics_filename' => ( is => 'rw', isa => 'Str', default => 'group_statisics.csv' ); | ||
| has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 ); | ||
| has 'clusters_filename' => ( is => 'rw', isa => 'Str' ); | ||
| has 'job_runner' => ( is => 'rw', isa => 'Str', default => 'LSF' ); | ||
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| sub BUILD { | ||
| my ($self) = @_; | ||
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| my ( $output_filename, $output_pan_geneome_filename, $job_runner, $output_statistics_filename, $output_multifasta_files, $clusters_filename, $fasta_files, $input_files, $help ); | ||
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| GetOptionsFromArray( | ||
| $self->args, | ||
| 'o|output=s' => \$output_filename, | ||
| 'j|job_runner=s' => \$job_runner, | ||
| 'output_multifasta_files' => \$output_multifasta_files, | ||
| 'p=s' => \$output_pan_geneome_filename, | ||
| 's=s' => \$output_statistics_filename, | ||
| 'c=s' => \$clusters_filename, | ||
| 'f=s@' => \$fasta_files, | ||
| 'i=s@' => \$input_files, | ||
| 'h|help' => \$help, | ||
| ); | ||
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| $self->job_runner($job_runner) if ( defined($job_runner) ); | ||
| $self->fasta_files($fasta_files) if (defined($fasta_files)); | ||
| $self->input_files($input_files) if (defined($input_files)); | ||
| $self->output_filename($output_filename) if (defined($output_filename)); | ||
| $self->output_pan_geneome_filename($output_pan_geneome_filename) if (defined($output_pan_geneome_filename)); | ||
| $self->output_statistics_filename($output_statistics_filename) if (defined($output_statistics_filename)); | ||
| $self->output_multifasta_files($output_multifasta_files) if (defined($output_multifasta_files)); | ||
| $self->clusters_filename($clusters_filename) if (defined($clusters_filename)); | ||
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| } | ||
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| sub run { | ||
| my ($self) = @_; | ||
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| ( !$self->help ) or die $self->usage_text; | ||
| if ( defined( $self->_error_message ) ) { | ||
| print $self->_error_message . "\n"; | ||
| die $self->usage_text; | ||
| } | ||
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| my $obj = Bio::PanGenome::PostAnalysis->new( | ||
| fasta_files => $self->fasta_files , | ||
| input_files => $self->input_files , | ||
| output_filename => $self->output_filename , | ||
| output_pan_geneome_filename => $self->output_pan_geneome_filename, | ||
| output_statistics_filename => $self->output_statistics_filename , | ||
| output_multifasta_files => $self->output_multifasta_files , | ||
| clusters_filename => $self->clusters_filename , | ||
| ); | ||
| $obj->run(); | ||
| } | ||
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| sub usage_text { | ||
| my ($self) = @_; | ||
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| return <<USAGE; | ||
| Usage: pan_genome_post_analysis [options] | ||
| Perform the post analysis on the pan genome. This script is usally only called by another script. | ||
| #Normal usage | ||
| pan_genome_post_analysis | ||
| -o output_groups_filename / | ||
| -p output_pan_genome_filename / | ||
| -s output_stats_filename / | ||
| -c output_clusters_filename / | ||
| -f proteins1.faa / | ||
| -f proteins2.faa / | ||
| -f proteins3.faa / | ||
| -i annotation1.gff / | ||
| -i annotation2.gff / | ||
| # This help message | ||
| pan_genome_post_analysis -h | ||
| USAGE | ||
| } | ||
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| __PACKAGE__->meta->make_immutable; | ||
| no Moose; | ||
| 1; |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,89 @@ | ||
| package Bio::PanGenome::External::PostAnalysis; | ||
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| # ABSTRACT: Perform the post analysis | ||
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| =head1 SYNOPSIS | ||
| Perform the post analysis | ||
| use Bio::PanGenome::External::PostAnalysis; | ||
| my $seg= Bio::PanGenome::External::PostAnalysis->new( | ||
| fasta_file => 'contigs.fa', | ||
| ); | ||
| $seg->run(); | ||
| =cut | ||
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| use Moose; | ||
| with 'Bio::PanGenome::JobRunner::Role'; | ||
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| has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); | ||
| has 'exec' => ( is => 'ro', isa => 'Str', default => 'pan_genome_post_analysis' ); | ||
| has 'fasta_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); | ||
| has 'output_filename' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
| has 'output_pan_geneome_filename' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
| has 'output_statistics_filename' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
| has 'clusters_filename' => ( is => 'ro', isa => 'Str', required => 1 ); | ||
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| # Overload Role | ||
| has '_memory_required_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__memory_required_in_mb' ); | ||
| has '_minimum_memory_mb' => ( is => 'ro', isa => 'Int', default => 1000 ); | ||
| has '_memory_per_sample_mb' => ( is => 'ro', isa => 'Int', default => 100 ); | ||
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| sub _build__memory_required_in_mb { | ||
| my ($self) = @_; | ||
| my $num_samples = @{ $self->input_files }; | ||
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| my $memory_required = $num_samples * $self->_memory_per_sample_mb; | ||
| if ( $memory_required < $self->_minimum_memory_mb ) { | ||
| $memory_required = $self->_minimum_memory_mb; | ||
| } | ||
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| return $memory_required; | ||
| } | ||
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| sub _command_to_run { | ||
| my ($self) = @_; | ||
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| my $fasta_files_param = join(' -f ',@{$self->fasta_files}); | ||
| $fasta_files_param = ' -f '.$fasta_files_param; | ||
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| my $input_files_param = join(' -i ',@{$self->input_files}); | ||
| $input_files_param = ' -i '.$input_files_param; | ||
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| return join( | ||
| " ", | ||
| ( | ||
| $self->exec, | ||
| '-o', $self->output_filename, | ||
| '-p', $self->output_pan_geneome_filename, | ||
| '-s', $self->output_statistics_filename, | ||
| '-c', $self->clusters_filename, | ||
| '--output_multifasta_files', | ||
| $fasta_files_param, | ||
| $input_files_param | ||
| ) | ||
| ); | ||
| } | ||
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| sub run { | ||
| my ($self) = @_; | ||
| my @commands_to_run; | ||
| push( @commands_to_run, $self->_command_to_run ); | ||
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| my $job_runner_obj = $self->_job_runner_class->new( | ||
| commands_to_run => \@commands_to_run, | ||
| memory_in_mb => $self->_memory_required_in_mb, | ||
| queue => $self->_queue, | ||
| dont_wait => $self->dont_wait, | ||
| ); | ||
| $job_runner_obj->run(); | ||
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| 1; | ||
| } | ||
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| no Moose; | ||
| __PACKAGE__->meta->make_immutable; | ||
| 1; |
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