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view Roary/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.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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undef $VERSION; package Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp; # ABSTRACT: Take in a FASTA file of proteins and blast against itself =head1 SYNOPSIS Take in a FASTA file of proteins and blast against itself =cut use Moose; use Getopt::Long qw(GetOptionsFromArray); use Bio::Roary::ParallelAllAgainstAllBlast; use Bio::Roary::CombinedProteome; use Bio::Roary::PrepareInputFiles; extends 'Bio::Roary::CommandLine::Common'; has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 ); has 'help' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'fasta_files' => ( is => 'rw', isa => 'ArrayRef' ); has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'blast_results' ); has 'job_runner' => ( is => 'rw', isa => 'Str', default => 'Local' ); has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 ); has 'makeblastdb_exec' => ( is => 'rw', isa => 'Str', default => 'makeblastdb' ); has 'blastp_exec' => ( is => 'rw', isa => 'Str', default => 'blastp' ); has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 ); has '_error_message' => ( is => 'rw', isa => 'Str' ); sub BUILD { my ($self) = @_; my ( $fasta_files, $output_filename, $job_runner, $makeblastdb_exec, $blastp_exec, $help, $cpus, $verbose, ); GetOptionsFromArray( $self->args, 'o|output=s' => \$output_filename, 'j|job_runner=s' => \$job_runner, 'm|makeblastdb_exec=s' => \$makeblastdb_exec, 'b|blastp_exec=s' => \$blastp_exec, 'p|processors=i' => \$cpus, 'v|verbose' => \$verbose, 'h|help' => \$help, ); if ( @{ $self->args } == 0 ) { $self->_error_message("Error: You need to provide a FASTA file"); } if ( defined($verbose) ) { $self->verbose($verbose); $self->logger->level(10000); } $self->help($help) if(defined($help)); $self->output_filename($output_filename) if ( defined($output_filename) ); $self->makeblastdb_exec($makeblastdb_exec) if ( defined($makeblastdb_exec) ); $self->blastp_exec($blastp_exec) if ( defined($blastp_exec) ); $self->job_runner($job_runner) if ( defined($job_runner) ); $self->cpus($cpus) if ( defined($cpus) ); if ( $self->cpus > 1 ) { $self->job_runner('Parallel'); } for my $filename ( @{ $self->args } ) { if ( !-e $filename ) { $self->_error_message("Error: Cant access file $filename"); last; } } $self->fasta_files( $self->args ); } sub run { my ($self) = @_; ( !$self->help ) or die $self->usage_text; if ( defined( $self->_error_message ) ) { print $self->_error_message . "\n"; die $self->usage_text; } my $prepare_input_files = Bio::Roary::PrepareInputFiles->new( input_files => $self->fasta_files, ); my $output_combined_filename; if(@{$self->fasta_files} > 1) { $output_combined_filename = 'combined_files.fa'; $self->logger->info("Combining protein files"); my $combine_fasta_files = Bio::Roary::CombinedProteome->new( proteome_files => $prepare_input_files->fasta_files, output_filename => $output_combined_filename, maximum_percentage_of_unknowns => 5.0, apply_unknowns_filter => 0 ); $combine_fasta_files->create_combined_proteome_file; } else { $output_combined_filename = $self->fasta_files->[0]; } $self->logger->info("Beginning all against all blast"); my $blast_obj = Bio::Roary::ParallelAllAgainstAllBlast->new( fasta_file => $output_combined_filename, blast_results_file_name => $self->output_filename, job_runner => $self->job_runner, cpus => $self->cpus, makeblastdb_exec => $self->makeblastdb_exec, blastp_exec => $self->blastp_exec, logger => $self->logger ); $blast_obj->run(); } sub usage_text { my ($self) = @_; return <<USAGE; Usage: parallel_all_against_all_blastp [options] file.faa Take in a FASTA file of proteins and blast against itself Options: -p INT number of threads [1] -o STR output filename for blast results [blast_results] -m STR makeblastdb executable [makeblastdb] -b STR blastp executable [blastp] -v verbose output to STDOUT -h this help message For further info see: http://sanger-pathogens.github.io/Roary/ USAGE } __PACKAGE__->meta->make_immutable; no Moose; 1;