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