File Coverage

lib/Bio/Roary/External/Mcl.pm
Criterion Covered Total %
statement 30 35 85.7
branch 4 6 66.6
condition n/a
subroutine 7 7 100.0
pod 0 1 0.0
total 41 49 83.6


line stmt bran cond sub pod time code
1             package Bio::Roary::External::Mcl;
2             $Bio::Roary::External::Mcl::VERSION = '3.11.0';
3             # ABSTRACT: Wrapper around MCL which takes in blast results and outputs clustered results
4              
5              
6 2     2   84568 use Moose;
  2         383570  
  2         11  
7 2     2   12085 use File::Which;
  2         786  
  2         762  
8             with 'Bio::Roary::JobRunner::Role';
9              
10             has 'blast_results' => ( is => 'ro', isa => 'Str', required => 1 );
11             has 'mcxdeblast_exec' => ( is => 'ro', isa => 'Str', default => 'mcxdeblast' );
12             has '_full_mcxdeblast_exec' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__full_mcxdeblast_exec');
13             has 'mcl_exec' => ( is => 'ro', isa => 'Str', default => 'mcl' );
14             has 'output_file' => ( is => 'ro', isa => 'Str', default => 'output_groups' );
15              
16             has '_score' => ( is => 'ro', isa => 'Str', default => 'r' );
17              
18             has 'inflation_value' => ( is => 'ro', isa => 'Num', default => 1.5 );
19             has '_logging' => ( is => 'ro', isa => 'Str', default => '> /dev/null 2>&1' );
20              
21             has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
22              
23             sub _build_memory_in_mb
24             {
25 1     1   2 my ($self) = @_;
26             # Todo: implement this equation for memory estimation if this hardcoded value proves too unstable.
27             # http://micans.org/mcl/man/mcl.html#opt-how-much-ram
28            
29 1         26 my $filename = $self->blast_results;
30 1         2 my $memory_required = 2000;
31 1 50       33 if(-e $filename)
32             {
33 0         0 $memory_required = -s $filename;
34             # Convert to mb
35 0         0 $memory_required = int($memory_required/1000000);
36             # increase memory for worst case senario
37 0         0 $memory_required *= 3;
38 0         0 $memory_required += 2000;
39             }
40              
41 1         27 return $memory_required;
42             }
43              
44              
45             sub _build__full_mcxdeblast_exec
46             {
47 2     2   6 my ($self) = @_;
48            
49 2 100       70 if(-e $self->mcxdeblast_exec)
50             {
51 1         21 return $self->mcxdeblast_exec;
52             }
53            
54 1         45 my $full_exec = which($self->mcxdeblast_exec);
55 1 50       343 if(! defined($full_exec))
56             {
57 1         49 $self->logger->error("Cannot find the mcxdeblast executable, please ensure its in your PATH") ;
58 1         645 exit();
59             }
60 0         0 return "perl $full_exec";
61             }
62              
63             sub _command_to_run {
64 4     4   10 my ($self) = @_;
65 4         140 return join(
66             " ",
67             (
68             $self->_full_mcxdeblast_exec, '-m9', '--score='.$self->_score,
69             '--line-mode=abc', $self->blast_results, '2> /dev/null',
70             '|', $self->mcl_exec, '-', '--abc',
71             '-I', $self->inflation_value, '-o', $self->output_file,
72             $self->_logging
73             )
74             );
75             }
76              
77             sub run {
78 2     2 0 5 my ($self) = @_;
79 2         6 my @commands_to_run;
80 2         6 push(@commands_to_run, $self->_command_to_run );
81 1         23 $self->logger->info( "Running command: " . $self->_command_to_run() );
82 1         44 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 );
83 1         5 $job_runner_obj->run();
84            
85 1         222 1;
86             }
87              
88 2     2   13 no Moose;
  2         4  
  2         12  
89             __PACKAGE__->meta->make_immutable;
90             1;
91              
92             __END__
93              
94             =pod
95              
96             =encoding UTF-8
97              
98             =head1 NAME
99              
100             Bio::Roary::External::Mcl - Wrapper around MCL which takes in blast results and outputs clustered results
101              
102             =head1 VERSION
103              
104             version 3.11.0
105              
106             =head1 SYNOPSIS
107              
108             Wrapper around MCL which takes in blast results and outputs clustered results
109              
110             use Bio::Roary::External::Mcl;
111            
112             my $mcl= Bio::Roary::External::Mcl->new(
113             blast_results => 'db',
114             mcxdeblast_exec => 'mcxdeblast',
115             mcl_exec => 'mcl',
116             output_file => 'output.groups'
117             );
118            
119             $mcl->run();
120              
121             =head1 AUTHOR
122              
123             Andrew J. Page <ap13@sanger.ac.uk>
124              
125             =head1 COPYRIGHT AND LICENSE
126              
127             This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
128              
129             This is free software, licensed under:
130              
131             The GNU General Public License, Version 3, June 2007
132              
133             =cut