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comparison Roary/lib/Bio/Roary/External/IterativeCdhit.pm @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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-1:000000000000 0:c47a5f61bc9f
1 package Bio::Roary::External::IterativeCdhit;
2
3 # ABSTRACT: Iteratively run CDhit
4
5 =head1 SYNOPSIS
6
7 Iteratively run CDhit
8
9 use Bio::Roary::External::IterativeCdhit;
10
11 my $seg= Bio::Roary::External::IterativeCdhit->new(
12 output_cd_hit_filename => '',
13 output_combined_filename => '',
14 number_of_input_files => 10,
15 output_filtered_clustered_fasta => '',
16 );
17
18 $seg->run();
19
20 =cut
21
22 use Moose;
23 with 'Bio::Roary::JobRunner::Role';
24
25 has 'output_cd_hit_filename' => ( is => 'ro', isa => 'Str', required => 1 );
26 has 'output_combined_filename' => ( is => 'ro', isa => 'Str', required => 1 );
27 has 'number_of_input_files' => ( is => 'ro', isa => 'Int', required => 1 );
28 has 'output_filtered_clustered_fasta' => ( is => 'ro', isa => 'Str', required => 1 );
29 has 'exec' => ( is => 'ro', isa => 'Str', default => 'iterative_cdhit' );
30 has '_max_cpus' => ( is => 'ro', isa => 'Int', default => 40 );
31 # Overload Role
32 has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
33
34 sub _build_memory_in_mb {
35 my ($self) = @_;
36 my $filename = $self->output_combined_filename;
37 my $memory_required = 2000;
38 if ( -e $filename ) {
39 $memory_required = -s $filename;
40
41 # Convert to mb
42 $memory_required = int( $memory_required / 1000000 );
43
44 # Pentuple memory for worst case senario
45 $memory_required *= 5;
46 $memory_required = 2000 if ( $memory_required < 2000 );
47 }
48
49 return $memory_required;
50 }
51
52 sub _build__max_available_memory_in_mb {
53 my ($self) = @_;
54 my $memory_to_cdhit = int( $self->memory_in_mb * 0.9 );
55 return $memory_to_cdhit;
56 }
57
58 sub _command_to_run {
59 my ($self) = @_;
60 my $cpus = ($self->cpus > $self->_max_cpus) ? $self->_max_cpus : $self->cpus;
61
62 return join(
63 ' ',
64 (
65 $self->exec, '-c', $self->output_cd_hit_filename, '-m',
66 $self->output_combined_filename, '-n', $self->number_of_input_files, '--cpus', $cpus, '-f',
67 $self->output_filtered_clustered_fasta
68 )
69 );
70 }
71
72 sub run {
73 my ($self) = @_;
74 my @commands_to_run;
75 push( @commands_to_run, $self->_command_to_run );
76 $self->logger->info( "Running command: " . $self->_command_to_run() );
77
78 my $job_runner_obj = $self->_job_runner_class->new(
79 commands_to_run => \@commands_to_run,
80 memory_in_mb => $self->memory_in_mb,
81 queue => $self->_queue,
82 cpus => $self->cpus
83 );
84 $job_runner_obj->run();
85
86 1;
87 }
88
89 no Moose;
90 __PACKAGE__->meta->make_immutable;
91
92 1;