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comparison Roary/lib/Bio/Roary/External/Fasttree.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::Fasttree;
2
3 # ABSTRACT: Wrapper to run Fasttree
4
5 =head1 SYNOPSIS
6
7 Wrapper to run cd-hit
8 use Bio::Roary::External::Fasttree;
9
10 my $obj = Bio::Roary::External::Fasttree->new(
11 input_file => 'abc.fa',
12 exec => 'Fasttree',
13 output_base => 'efg',
14 );
15 $obj->run;
16
17 =cut
18
19 use Moose;
20 with 'Bio::Roary::JobRunner::Role';
21
22 has 'input_file' => ( is => 'ro', isa => 'Str', required => 1 );
23 has 'output_file' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_output_file' );
24 has 'exec' => ( is => 'ro', isa => 'Str', default => 'FastTree' );
25 has 'alt_exec' => ( is => 'ro', isa => 'Str', default => 'fasttree' );
26 has '_logging' => ( is => 'ro', isa => 'Str', default => '2> /dev/null' );
27
28 sub _build_output_file
29 {
30 my ($self) = @_;
31 return $self->input_file.".newick";
32 }
33
34 sub _command_to_run {
35 my ($self) = @_;
36
37 my $executable = $self->_find_exe([$self->exec, $self->alt_exec]);
38 my $logging_str = "";
39 $logging_str = $self->_logging if(! $self->verbose);
40
41 return join(
42 ' ', ($executable, '-fastest', '-nt', $self->input_file, '>', $self->output_file, $logging_str)
43 );
44 }
45
46 sub run {
47 my ($self) = @_;
48 my @commands_to_run;
49
50 if(!defined($self->input_file) || ! ( -e $self->input_file))
51 {
52 $self->logger->error( "The input file is missing so not creating a tree" );
53 return 1;
54 }
55
56 if(-s $self->input_file < 5)
57 {
58 $self->logger->info( "The input file is too small so not creating a tree" );
59 return 1;
60 }
61
62 push(@commands_to_run, $self->_command_to_run() );
63 $self->logger->info( "Running command: " . $self->_command_to_run() );
64 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 );
65 $job_runner_obj->run();
66
67 1;
68 }
69
70 no Moose;
71 __PACKAGE__->meta->make_immutable;
72
73 1;