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1 undef $VERSION;
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2 package Bio::Roary::CommandLine::RoaryReorderSpreadsheet;
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3
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4 # ABSTRACT: Take in a tree and a spreadsheet and output a reordered spreadsheet
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5
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6 =head1 SYNOPSIS
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7
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8 Take in a tree and a spreadsheet and output a reordered spreadsheet
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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::ReorderSpreadsheet;
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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
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21 has 'tree_file' => ( is => 'rw', isa => 'Str' );
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22 has 'spreadsheet_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' );
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23 has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'reordered_spreadsheet.csv' );
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24 has 'tree_format' => ( is => 'rw', isa => 'Str', default => 'newick' );
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25 has 'search_strategy' => ( is => 'rw', isa => 'Str', default => 'depth' );
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26 has 'sortby' => ( is => 'rw', isa => 'Str', default => 'height');
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27 has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
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28
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29
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30 sub BUILD {
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31 my ($self) = @_;
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32
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33 my ( $output_filename, $tree_file,$search_strategy, $sortby, $tree_format, $spreadsheet_filename,$verbose, $help );
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34
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35 GetOptionsFromArray(
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36 $self->args,
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37 'o|output_filename=s' => \$output_filename,
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38 't|tree_file=s' => \$tree_file,
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39 'f|tree_format=s' => \$tree_format,
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40 's|spreadsheet_filename=s' => \$spreadsheet_filename,
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41 'a|search_strategy=s' => \$search_strategy,
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42 'b|sortby=s' => \$sortby,
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43 'v|verbose' => \$verbose,
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44 'h|help' => \$help,
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45 );
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46
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47 if ( defined($verbose) ) {
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48 $self->verbose($verbose);
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49 $self->logger->level(10000);
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50 }
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51 $self->help($help) if(defined($help));
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52 $self->output_filename($output_filename) if ( defined($output_filename) );
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53 $self->tree_file($tree_file) if ( defined($tree_file) );
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54 $self->tree_format($tree_format) if ( defined($tree_format) );
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55 $self->spreadsheet_filename($spreadsheet_filename) if ( defined($spreadsheet_filename) );
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56 $self->sortby($sortby) if ( defined($sortby) );
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57 $self->search_strategy($search_strategy) if ( defined($search_strategy) );
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58 }
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59
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60 sub run {
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61 my ($self) = @_;
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62 ( defined($self->spreadsheet_filename) && defined($self->tree_file) && ( -e $self->spreadsheet_filename ) && ( -e $self->tree_file ) && ( !$self->help ) ) or die $self->usage_text;
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63
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64 ($self->sortby eq "height" || $self->sortby eq "creation" || $self->sortby eq "alpha" || $self->sortby eq "revalpha") or die $self->usage_text;
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65 ($self->search_strategy eq "breadth" || $self->search_strategy eq "depth") or die $self->usage_text;
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66
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67 my $obj = Bio::Roary::ReorderSpreadsheet->new(
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68 tree_file => $self->tree_file,
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69 spreadsheet => $self->spreadsheet_filename,
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70 output_filename => $self->output_filename,
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71 sortby => $self->sortby,
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72 search_strategy => $self->search_strategy
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73 );
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74 $obj->reorder_spreadsheet();
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75
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76 }
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77
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78 sub usage_text {
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79 my ($self) = @_;
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80
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81 return <<USAGE;
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82 Usage: pan_genome_reorder_spreadsheet [options] -t tree.newick
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83 Reorder the columns in the gene presence and absence spreadsheet against a phylogenetic tree.
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84
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85 Options: -t STR tree filename []
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86 -o STR output filename [reordered_spreadsheet.csv]
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87 -f STR tree format (newick/nexus/nhx/svggraph/tabtree/lintree) [newick]
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88 -s STR input gene presence and absence spreadsheet [gene_presence_absence.csv]
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89 -a STR search strategy (depth/breadth) [depth]
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90 -b STR sorting method (height/creation/alpha/revalpha) [height]
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91 -v verbose output to STDOUT
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92 -h this help message
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93
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94 For further info see: http://sanger-pathogens.github.io/Roary/
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95 USAGE
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96 }
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97
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98 __PACKAGE__->meta->make_immutable;
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99 no Moose;
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100 1;
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