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view Roary/lib/Bio/Roary/CommandLine/IterativeCdhit.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 $VERSION; package Bio::Roary::CommandLine::IterativeCdhit; # ABSTRACT: Iteratively run cdhit =head1 SYNOPSIS Iteratively run cdhit =cut use Moose; use Getopt::Long qw(GetOptionsFromArray); use Bio::Roary::IterativeCdhit; extends 'Bio::Roary::CommandLine::Common'; has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 ); has 'help' => ( is => 'rw', isa => 'Bool', default => 0 ); has '_error_message' => ( is => 'rw', isa => 'Str' ); has 'output_cd_hit_filename' => ( is => 'rw', isa => 'Str', default => '_clustered' ); has 'output_combined_filename' => ( is => 'rw', isa => 'Str', default => '_combined_files' ); has 'number_of_input_files' => ( is => 'rw', isa => 'Int', default => 1 ); has 'output_filtered_clustered_fasta' => ( is => 'rw', isa => 'Str', default => '_clustered_filtered.fa' ); has 'lower_bound_percentage' => ( is => 'rw', isa => 'Num', default => 0.98 ); has 'upper_bound_percentage' => ( is => 'rw', isa => 'Num', default => 0.99 ); has 'step_size_percentage' => ( is => 'rw', isa => 'Num', default => 0.005 ); has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 ); has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 ); sub BUILD { my ($self) = @_; my ( $output_cd_hit_filename,$cpus,$lower_bound_percentage,$upper_bound_percentage,$step_size_percentage, $output_combined_filename, $number_of_input_files, $output_filtered_clustered_fasta,$verbose, $help ); GetOptionsFromArray( $self->args, 'c|output_cd_hit_filename=s' => \$output_cd_hit_filename, 'm|output_combined_filename=s' => \$output_combined_filename, 'n|number_of_input_files=i' => \$number_of_input_files, 'f|output_filtered_clustered_fasta=s' => \$output_filtered_clustered_fasta, 'l|lower_bound_percentage=s' => \$lower_bound_percentage, 'u|upper_bound_percentage=s' => \$upper_bound_percentage, 's|step_size_percentage=s' => \$step_size_percentage, 'p|cpus=i' => \$cpus, 'v|verbose' => \$verbose, 'h|help' => \$help, ); if ( defined($verbose) ) { $self->verbose($verbose); $self->logger->level(10000); } $self->help($help) if(defined($help)); $self->lower_bound_percentage($lower_bound_percentage/100) if ( defined($lower_bound_percentage) ); $self->upper_bound_percentage($upper_bound_percentage/100) if ( defined($upper_bound_percentage) ); $self->step_size_percentage($step_size_percentage/100) if ( defined($step_size_percentage) ); $self->output_cd_hit_filename($output_cd_hit_filename) if ( defined($output_cd_hit_filename) ); $self->output_combined_filename($output_combined_filename) if ( defined($output_combined_filename) ); $self->number_of_input_files($number_of_input_files) if ( defined($number_of_input_files) ); $self->cpus($cpus) if ( defined($cpus) ); $self->output_filtered_clustered_fasta($output_filtered_clustered_fasta) if ( defined($output_filtered_clustered_fasta) ); } sub run { my ($self) = @_; ( !$self->help ) or die $self->usage_text; if ( defined( $self->_error_message ) ) { print $self->_error_message . "\n"; die $self->usage_text; } my $obj = Bio::Roary::IterativeCdhit->new( output_cd_hit_filename => $self->output_cd_hit_filename, output_combined_filename => $self->output_combined_filename, number_of_input_files => $self->number_of_input_files, output_filtered_clustered_fasta => $self->output_filtered_clustered_fasta, lower_bound_percentage => $self->lower_bound_percentage, upper_bound_percentage => $self->upper_bound_percentage, step_size_percentage => $self->step_size_percentage, cpus => $self->cpus, logger => $self->logger ); $obj->run; } sub usage_text { my ($self) = @_; return <<USAGE; Usage: iterative_cdhit [options] Iteratively cluster a FASTA file of proteins with CD-hit, lower the threshold each time and extracting core genes (1 per isolate) to another file, and remove them from the input proteins file. Required arguments: -m STR input FASTA file of protein sequences [_combined_files] Options: -p INT number of threads [1] -n INT number of isolates [1] -c STR cd-hit output filename [_clustered] -f STR output filename for filtered sequences [_clustered_filtered.fa] -l FLOAT lower bound percentage identity [98.0] -u FLOAT upper bound percentage identity [99.0] -s FLOAT step size for percentage identity [0.5] -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;