diff Roary/lib/Bio/Roary.pm @ 0:c47a5f61bc9f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/lib/Bio/Roary.pm	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,150 @@
+package Bio::Roary;
+
+# ABSTRACT: Create a pan genome
+
+=head1 SYNOPSIS
+
+Create a pan genome
+
+=cut
+
+use Moose;
+use File::Copy;
+use Bio::Perl;
+use Bio::Roary::ParallelAllAgainstAllBlast;
+use Bio::Roary::CombinedProteome;
+use Bio::Roary::External::Cdhit;
+use Bio::Roary::External::Mcl;
+use Bio::Roary::InflateClusters;
+use Bio::Roary::AnalyseGroups;
+use Bio::Roary::GroupLabels;
+use Bio::Roary::AnnotateGroups;
+use Bio::Roary::GroupStatistics;
+use Bio::Roary::Output::GroupsMultifastasNucleotide;
+use Bio::Roary::External::PostAnalysis;
+use Bio::Roary::FilterFullClusters;
+use Bio::Roary::External::IterativeCdhit;
+use Bio::Roary::Output::BlastIdentityFrequency;
+
+has 'fasta_files'                 => ( is => 'rw', isa => 'ArrayRef', required => 1 );
+has 'input_files'                 => ( is => 'rw', isa => 'ArrayRef', required => 1 );
+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  => 'gene_presence_absence.csv' );
+has 'job_runner'                  => ( is => 'rw', isa => 'Str',      default  => 'Local' );
+has 'cpus'                        => ( is => 'ro', isa => 'Int',      default  => 1 );
+has 'makeblastdb_exec'            => ( is => 'rw', isa => 'Str',      default  => 'makeblastdb' );
+has 'blastp_exec'                 => ( is => 'rw', isa => 'Str',      default  => 'blastp' );
+has 'mcxdeblast_exec'             => ( is => 'ro', isa => 'Str',      default  => 'mcxdeblast' );
+has 'mcl_exec'                    => ( is => 'ro', isa => 'Str',      default  => 'mcl' );
+has 'perc_identity'               => ( is => 'ro', isa => 'Num',      default  => 98 );
+has 'dont_delete_files'           => ( is => 'ro', isa => 'Bool',     default  => 0 );
+has 'dont_create_rplots'          => ( is => 'rw', isa => 'Bool',     default  => 0 );
+has 'dont_split_groups'           => ( is => 'ro', isa => 'Bool',     default  => 0 );
+has 'verbose_stats'               => ( is => 'rw', isa => 'Bool',     default  => 0 );
+has 'translation_table'           => ( is => 'rw', isa => 'Int',      default  => 11 );
+has 'group_limit'                 => ( is => 'rw', isa => 'Num',      default  => 50000 );
+has 'core_definition'             => ( is => 'rw', isa => 'Num',      default  => 1.0 );
+has 'verbose'                     => ( is => 'rw', isa => 'Bool',     default  => 0 );
+has 'mafft'                       => ( is => 'ro', isa => 'Bool',     default  => 0 );
+has 'inflation_value'             => ( is => 'rw', isa => 'Num',      default  => 1.5 );
+has 'allow_paralogs'              => ( is => 'rw', isa => 'Bool',     default => 0 );
+
+has 'output_multifasta_files' => ( is => 'ro', isa => 'Bool', default => 0 );
+
+sub run {
+    my ($self) = @_;
+
+    my $output_combined_filename      = '_combined_files';
+    my $output_cd_hit_filename        = '_clustered';
+    my $output_blast_results_filename = '_blast_results';
+    my $output_mcl_filename           = '_uninflated_mcl_groups';
+    my $output_filtered_clustered_fasta  = '_clustered_filtered.fa';
+    my $cdhit_groups = $output_combined_filename.'.groups';
+    
+    
+    unlink($cdhit_groups) unless($self->dont_delete_files == 1);
+
+	print "Combine proteins into a single file\n" if($self->verbose);
+    my $combine_fasta_files = Bio::Roary::CombinedProteome->new(
+        proteome_files  => $self->fasta_files,
+        output_filename => $output_combined_filename,
+    );
+    $combine_fasta_files->create_combined_proteome_file;
+
+    my $number_of_input_files = @{$self->input_files};
+
+	print "Iteratively run cd-hit\n" if($self->verbose);
+    my $iterative_cdhit= Bio::Roary::External::IterativeCdhit->new(
+      output_cd_hit_filename           => $output_cd_hit_filename,
+      output_combined_filename         => $output_combined_filename,
+      number_of_input_files            => $number_of_input_files, 
+      output_filtered_clustered_fasta  => $output_filtered_clustered_fasta,
+      job_runner                       => $self->job_runner,
+      cpus                             => $self->cpus
+    );
+    
+    $iterative_cdhit->run();
+
+	print "Parallel all against all blast\n" if($self->verbose);
+    my $blast_obj = Bio::Roary::ParallelAllAgainstAllBlast->new(
+        fasta_file              => $output_cd_hit_filename,
+        blast_results_file_name => $output_blast_results_filename,
+        job_runner              => $self->job_runner,
+        cpus                    => $self->cpus,
+        makeblastdb_exec        => $self->makeblastdb_exec,
+        blastp_exec             => $self->blastp_exec,
+        perc_identity           => $self->perc_identity
+    );
+    $blast_obj->run();
+    
+    my $blast_identity_frequency_obj = Bio::Roary::Output::BlastIdentityFrequency->new(
+        input_filename      => $output_blast_results_filename,
+      );
+    $blast_identity_frequency_obj->create_file();
+
+	print "Cluster with MCL\n" if($self->verbose);
+    my $mcl = Bio::Roary::External::Mcl->new(
+        blast_results   => $output_blast_results_filename,
+        mcxdeblast_exec => $self->mcxdeblast_exec,
+        mcl_exec        => $self->mcl_exec,
+        job_runner      => $self->job_runner,
+        cpus            => $self->cpus,
+	inflation_value => $self->inflation_value,
+        output_file     => $output_mcl_filename
+    );
+    $mcl->run();
+
+    unlink($output_blast_results_filename) unless($self->dont_delete_files == 1);
+    
+    my $post_analysis = Bio::Roary::External::PostAnalysis->new(
+        job_runner                  => 'Local',
+        cpus                        => $self->cpus,
+        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,
+        clusters_filename           => $output_cd_hit_filename.'.clstr',
+        dont_wait                   => 1,
+        output_multifasta_files     => $self->output_multifasta_files,
+        dont_delete_files           => $self->dont_delete_files,
+        dont_create_rplots          => $self->dont_create_rplots,
+        dont_split_groups           => $self->dont_split_groups,
+        verbose_stats               => $self->verbose_stats,
+        translation_table           => $self->translation_table,
+        group_limit                 => $self->group_limit,
+        core_definition             => $self->core_definition,
+		verbose                     => $self->verbose,
+		mafft                       => $self->mafft,
+		allow_paralogs              => $self->allow_paralogs,
+    );
+    $post_analysis->run();
+
+}
+
+
+no Moose;
+__PACKAGE__->meta->make_immutable;
+
+1;