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1 package Bio::Roary::External::Cdhit;
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2
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3 # ABSTRACT: Wrapper to run cd-hit
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4
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5 =head1 SYNOPSIS
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6
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7 Wrapper to run cd-hit
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8 use Bio::Roary::External::Cdhit;
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9
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10 my $obj = Bio::Roary::External::Cdhit->new(
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11 input_file => 'abc.fa',
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12 exec => 'cd-hit',
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13 output_base => 'efg',
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14 );
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15 $obj->run;
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16
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17 =cut
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18
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19 use Moose;
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20
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21 with 'Bio::Roary::JobRunner::Role';
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22
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23 has 'input_file' => ( is => 'ro', isa => 'Str', required => 1 );
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24 has 'output_base' => ( is => 'ro', isa => 'Str', default => 'output' );
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25 has 'exec' => ( is => 'ro', isa => 'Str', default => 'cd-hit' );
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26 has 'alt_exec' => ( is => 'ro', isa => 'Str', default => 'cdhit' );
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27 has '_max_available_memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__max_available_memory_in_mb' );
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28 has '_use_most_similar_clustering' => ( is => 'ro', isa => 'Bool', default => 1 );
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29 has '_length_difference_cutoff' => ( is => 'ro', isa => 'Num', default => 1 );
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30 has '_sequence_identity_threshold' => ( is => 'ro', isa => 'Num', default => 1 );
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31 has '_description_length' => ( is => 'ro', isa => 'Int', default => 256 );
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32 has '_logging' => ( is => 'ro', isa => 'Str', default => '> /dev/null 2>&1' );
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33 has '_max_cpus' => ( is => 'ro', isa => 'Int', default => 40 );
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34
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35
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36 # Overload Role
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37 has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
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38
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39 sub _build_memory_in_mb
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40 {
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41 my ($self) = @_;
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42 my $filename = $self->input_file;
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43 my $memory_required = 2000;
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44 if(-e $filename)
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45 {
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46 $memory_required = -s $filename;
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47 # Convert to mb
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48 $memory_required = int($memory_required/1000000);
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49 # Give it bucket loads of memory for the worst case scenario
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50 $memory_required *= 5;
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51 $memory_required = 2000 if($memory_required < 2000);
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52 }
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53
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54 return $memory_required;
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55 }
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56
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57 sub _build__max_available_memory_in_mb
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58 {
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59 my ($self) = @_;
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60 my $memory_to_cdhit = int($self->memory_in_mb *0.9);
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61 return $memory_to_cdhit;
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62 }
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63
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64 sub clusters_filename
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65 {
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66 my ($self) = @_;
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67 return join('.',($self->output_base,'clstr'));
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68 }
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69
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70 sub _command_to_run {
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71 my ($self) = @_;
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72
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73 my $executable = $self->_find_exe([$self->exec, $self->alt_exec]);
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74
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75 my $cpus = ($self->cpus > $self->_max_cpus) ? $self->_max_cpus : $self->cpus;
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76 return join(
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77 ' ',
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78 (
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79 $executable, '-i', $self->input_file, '-o',
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80 $self->output_base, '-T', $cpus, '-M',
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81 $self->_max_available_memory_in_mb, '-g', $self->_use_most_similar_clustering, '-s',
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82 $self->_length_difference_cutoff, '-d', $self->_description_length ,'-c', $self->_sequence_identity_threshold,
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83 $self->_logging
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84 )
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85 );
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86 }
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87
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88 sub run {
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89 my ($self) = @_;
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90 my @commands_to_run;
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91
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92 push(@commands_to_run, $self->_command_to_run() );
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93 $self->logger->info( "Running command: " . $self->_command_to_run() );
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94 my $job_runner_obj = $self->_job_runner_class->new( commands_to_run => \@commands_to_run, memory_in_mb => $self->memory_in_mb, queue => $self->_queue, cpus => $self->cpus );
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95 $job_runner_obj->run();
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96
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97 1;
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98 }
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99
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100 no Moose;
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101 __PACKAGE__->meta->make_immutable;
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102
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103 1;
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