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1 package Bio::Roary::External::IterativeCdhit;
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2
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3 # ABSTRACT: Iteratively run CDhit
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4
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5 =head1 SYNOPSIS
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6
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7 Iteratively run CDhit
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8
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9 use Bio::Roary::External::IterativeCdhit;
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10
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11 my $seg= Bio::Roary::External::IterativeCdhit->new(
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12 output_cd_hit_filename => '',
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13 output_combined_filename => '',
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14 number_of_input_files => 10,
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15 output_filtered_clustered_fasta => '',
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16 );
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17
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18 $seg->run();
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19
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20 =cut
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21
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22 use Moose;
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23 with 'Bio::Roary::JobRunner::Role';
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24
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25 has 'output_cd_hit_filename' => ( is => 'ro', isa => 'Str', required => 1 );
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26 has 'output_combined_filename' => ( is => 'ro', isa => 'Str', required => 1 );
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27 has 'number_of_input_files' => ( is => 'ro', isa => 'Int', required => 1 );
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28 has 'output_filtered_clustered_fasta' => ( is => 'ro', isa => 'Str', required => 1 );
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29 has 'exec' => ( is => 'ro', isa => 'Str', default => 'iterative_cdhit' );
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30 has '_max_cpus' => ( is => 'ro', isa => 'Int', default => 40 );
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31 # Overload Role
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32 has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
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33
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34 sub _build_memory_in_mb {
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35 my ($self) = @_;
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36 my $filename = $self->output_combined_filename;
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37 my $memory_required = 2000;
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38 if ( -e $filename ) {
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39 $memory_required = -s $filename;
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40
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41 # Convert to mb
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42 $memory_required = int( $memory_required / 1000000 );
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43
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44 # Pentuple memory for worst case senario
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45 $memory_required *= 5;
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46 $memory_required = 2000 if ( $memory_required < 2000 );
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47 }
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48
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49 return $memory_required;
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50 }
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51
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52 sub _build__max_available_memory_in_mb {
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53 my ($self) = @_;
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54 my $memory_to_cdhit = int( $self->memory_in_mb * 0.9 );
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55 return $memory_to_cdhit;
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56 }
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57
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58 sub _command_to_run {
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59 my ($self) = @_;
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60 my $cpus = ($self->cpus > $self->_max_cpus) ? $self->_max_cpus : $self->cpus;
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61
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62 return join(
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63 ' ',
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64 (
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65 $self->exec, '-c', $self->output_cd_hit_filename, '-m',
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66 $self->output_combined_filename, '-n', $self->number_of_input_files, '--cpus', $cpus, '-f',
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67 $self->output_filtered_clustered_fasta
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68 )
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69 );
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70 }
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71
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72 sub run {
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73 my ($self) = @_;
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74 my @commands_to_run;
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75 push( @commands_to_run, $self->_command_to_run );
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76 $self->logger->info( "Running command: " . $self->_command_to_run() );
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77
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78 my $job_runner_obj = $self->_job_runner_class->new(
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79 commands_to_run => \@commands_to_run,
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80 memory_in_mb => $self->memory_in_mb,
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81 queue => $self->_queue,
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82 cpus => $self->cpus
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83 );
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84 $job_runner_obj->run();
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85
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86 1;
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87 }
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88
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89 no Moose;
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90 __PACKAGE__->meta->make_immutable;
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91
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92 1;
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