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comparison Roary/lib/Bio/Roary/CommandLine/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 undef $VERSION;
2 package Bio::Roary::CommandLine::IterativeCdhit;
3
4 # ABSTRACT: Iteratively run cdhit
5
6 =head1 SYNOPSIS
7
8 Iteratively run cdhit
9
10 =cut
11
12 use Moose;
13 use Getopt::Long qw(GetOptionsFromArray);
14 use Bio::Roary::IterativeCdhit;
15 extends 'Bio::Roary::CommandLine::Common';
16
17 has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
18 has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
19 has 'help' => ( is => 'rw', isa => 'Bool', default => 0 );
20 has '_error_message' => ( is => 'rw', isa => 'Str' );
21
22 has 'output_cd_hit_filename' => ( is => 'rw', isa => 'Str', default => '_clustered' );
23 has 'output_combined_filename' => ( is => 'rw', isa => 'Str', default => '_combined_files' );
24 has 'number_of_input_files' => ( is => 'rw', isa => 'Int', default => 1 );
25 has 'output_filtered_clustered_fasta' => ( is => 'rw', isa => 'Str', default => '_clustered_filtered.fa' );
26
27 has 'lower_bound_percentage' => ( is => 'rw', isa => 'Num', default => 0.98 );
28 has 'upper_bound_percentage' => ( is => 'rw', isa => 'Num', default => 0.99 );
29 has 'step_size_percentage' => ( is => 'rw', isa => 'Num', default => 0.005 );
30 has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 );
31 has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
32
33
34 sub BUILD {
35 my ($self) = @_;
36
37 my ( $output_cd_hit_filename,$cpus,$lower_bound_percentage,$upper_bound_percentage,$step_size_percentage, $output_combined_filename, $number_of_input_files, $output_filtered_clustered_fasta,$verbose,
38 $help );
39
40 GetOptionsFromArray(
41 $self->args,
42 'c|output_cd_hit_filename=s' => \$output_cd_hit_filename,
43 'm|output_combined_filename=s' => \$output_combined_filename,
44 'n|number_of_input_files=i' => \$number_of_input_files,
45 'f|output_filtered_clustered_fasta=s' => \$output_filtered_clustered_fasta,
46 'l|lower_bound_percentage=s' => \$lower_bound_percentage,
47 'u|upper_bound_percentage=s' => \$upper_bound_percentage,
48 's|step_size_percentage=s' => \$step_size_percentage,
49 'p|cpus=i' => \$cpus,
50 'v|verbose' => \$verbose,
51 'h|help' => \$help,
52 );
53
54 if ( defined($verbose) ) {
55 $self->verbose($verbose);
56 $self->logger->level(10000);
57 }
58 $self->help($help) if(defined($help));
59 $self->lower_bound_percentage($lower_bound_percentage/100) if ( defined($lower_bound_percentage) );
60 $self->upper_bound_percentage($upper_bound_percentage/100) if ( defined($upper_bound_percentage) );
61 $self->step_size_percentage($step_size_percentage/100) if ( defined($step_size_percentage) );
62 $self->output_cd_hit_filename($output_cd_hit_filename) if ( defined($output_cd_hit_filename) );
63 $self->output_combined_filename($output_combined_filename) if ( defined($output_combined_filename) );
64 $self->number_of_input_files($number_of_input_files) if ( defined($number_of_input_files) );
65 $self->cpus($cpus) if ( defined($cpus) );
66 $self->output_filtered_clustered_fasta($output_filtered_clustered_fasta)
67 if ( defined($output_filtered_clustered_fasta) );
68
69 }
70
71 sub run {
72 my ($self) = @_;
73
74 ( !$self->help ) or die $self->usage_text;
75 if ( defined( $self->_error_message ) ) {
76 print $self->_error_message . "\n";
77 die $self->usage_text;
78 }
79
80 my $obj = Bio::Roary::IterativeCdhit->new(
81 output_cd_hit_filename => $self->output_cd_hit_filename,
82 output_combined_filename => $self->output_combined_filename,
83 number_of_input_files => $self->number_of_input_files,
84 output_filtered_clustered_fasta => $self->output_filtered_clustered_fasta,
85 lower_bound_percentage => $self->lower_bound_percentage,
86 upper_bound_percentage => $self->upper_bound_percentage,
87 step_size_percentage => $self->step_size_percentage,
88 cpus => $self->cpus,
89 logger => $self->logger
90
91 );
92 $obj->run;
93 }
94
95 sub usage_text {
96 my ($self) = @_;
97
98 return <<USAGE;
99 Usage: iterative_cdhit [options]
100 Iteratively cluster a FASTA file of proteins with CD-hit, lower the threshold each time and extracting core genes (1 per isolate) to another file, and remove them from the input proteins file.
101
102 Required arguments:
103 -m STR input FASTA file of protein sequences [_combined_files]
104
105 Options: -p INT number of threads [1]
106 -n INT number of isolates [1]
107 -c STR cd-hit output filename [_clustered]
108 -f STR output filename for filtered sequences [_clustered_filtered.fa]
109 -l FLOAT lower bound percentage identity [98.0]
110 -u FLOAT upper bound percentage identity [99.0]
111 -s FLOAT step size for percentage identity [0.5]
112 -v verbose output to STDOUT
113 -h this help message
114
115 For further info see: http://sanger-pathogens.github.io/Roary/
116 USAGE
117 }
118
119 __PACKAGE__->meta->make_immutable;
120 no Moose;
121 1;