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lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm  view on Meta::CPAN

undef $VERSION;
package Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp;
$Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp::VERSION = '3.13.0';
# ABSTRACT: Take in a FASTA file of proteins and blast against itself


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) = @_;