0
|
1 undef $VERSION;
|
|
2 package Bio::Roary::CommandLine::RoaryReorderSpreadsheet;
|
|
3
|
|
4 # ABSTRACT: Take in a tree and a spreadsheet and output a reordered spreadsheet
|
|
5
|
|
6 =head1 SYNOPSIS
|
|
7
|
|
8 Take in a tree and a spreadsheet and output a reordered spreadsheet
|
|
9
|
|
10 =cut
|
|
11
|
|
12 use Moose;
|
|
13 use Getopt::Long qw(GetOptionsFromArray);
|
|
14 use Bio::Roary::ReorderSpreadsheet;
|
|
15 extends 'Bio::Roary::CommandLine::Common';
|
|
16
|
|
17 has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
|
|
18 has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
|
|
19 has 'help' => ( is => 'rw', isa => 'Bool', default => 0 );
|
|
20
|
|
21 has 'tree_file' => ( is => 'rw', isa => 'Str' );
|
|
22 has 'spreadsheet_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' );
|
|
23 has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'reordered_spreadsheet.csv' );
|
|
24 has 'tree_format' => ( is => 'rw', isa => 'Str', default => 'newick' );
|
|
25 has 'search_strategy' => ( is => 'rw', isa => 'Str', default => 'depth' );
|
|
26 has 'sortby' => ( is => 'rw', isa => 'Str', default => 'height');
|
|
27 has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
|
|
28
|
|
29
|
|
30 sub BUILD {
|
|
31 my ($self) = @_;
|
|
32
|
|
33 my ( $output_filename, $tree_file,$search_strategy, $sortby, $tree_format, $spreadsheet_filename,$verbose, $help );
|
|
34
|
|
35 GetOptionsFromArray(
|
|
36 $self->args,
|
|
37 'o|output_filename=s' => \$output_filename,
|
|
38 't|tree_file=s' => \$tree_file,
|
|
39 'f|tree_format=s' => \$tree_format,
|
|
40 's|spreadsheet_filename=s' => \$spreadsheet_filename,
|
|
41 'a|search_strategy=s' => \$search_strategy,
|
|
42 'b|sortby=s' => \$sortby,
|
|
43 'v|verbose' => \$verbose,
|
|
44 'h|help' => \$help,
|
|
45 );
|
|
46
|
|
47 if ( defined($verbose) ) {
|
|
48 $self->verbose($verbose);
|
|
49 $self->logger->level(10000);
|
|
50 }
|
|
51 $self->help($help) if(defined($help));
|
|
52 $self->output_filename($output_filename) if ( defined($output_filename) );
|
|
53 $self->tree_file($tree_file) if ( defined($tree_file) );
|
|
54 $self->tree_format($tree_format) if ( defined($tree_format) );
|
|
55 $self->spreadsheet_filename($spreadsheet_filename) if ( defined($spreadsheet_filename) );
|
|
56 $self->sortby($sortby) if ( defined($sortby) );
|
|
57 $self->search_strategy($search_strategy) if ( defined($search_strategy) );
|
|
58 }
|
|
59
|
|
60 sub run {
|
|
61 my ($self) = @_;
|
|
62 ( defined($self->spreadsheet_filename) && defined($self->tree_file) && ( -e $self->spreadsheet_filename ) && ( -e $self->tree_file ) && ( !$self->help ) ) or die $self->usage_text;
|
|
63
|
|
64 ($self->sortby eq "height" || $self->sortby eq "creation" || $self->sortby eq "alpha" || $self->sortby eq "revalpha") or die $self->usage_text;
|
|
65 ($self->search_strategy eq "breadth" || $self->search_strategy eq "depth") or die $self->usage_text;
|
|
66
|
|
67 my $obj = Bio::Roary::ReorderSpreadsheet->new(
|
|
68 tree_file => $self->tree_file,
|
|
69 spreadsheet => $self->spreadsheet_filename,
|
|
70 output_filename => $self->output_filename,
|
|
71 sortby => $self->sortby,
|
|
72 search_strategy => $self->search_strategy
|
|
73 );
|
|
74 $obj->reorder_spreadsheet();
|
|
75
|
|
76 }
|
|
77
|
|
78 sub usage_text {
|
|
79 my ($self) = @_;
|
|
80
|
|
81 return <<USAGE;
|
|
82 Usage: pan_genome_reorder_spreadsheet [options] -t tree.newick
|
|
83 Reorder the columns in the gene presence and absence spreadsheet against a phylogenetic tree.
|
|
84
|
|
85 Options: -t STR tree filename []
|
|
86 -o STR output filename [reordered_spreadsheet.csv]
|
|
87 -f STR tree format (newick/nexus/nhx/svggraph/tabtree/lintree) [newick]
|
|
88 -s STR input gene presence and absence spreadsheet [gene_presence_absence.csv]
|
|
89 -a STR search strategy (depth/breadth) [depth]
|
|
90 -b STR sorting method (height/creation/alpha/revalpha) [height]
|
|
91 -v verbose output to STDOUT
|
|
92 -h this help message
|
|
93
|
|
94 For further info see: http://sanger-pathogens.github.io/Roary/
|
|
95 USAGE
|
|
96 }
|
|
97
|
|
98 __PACKAGE__->meta->make_immutable;
|
|
99 no Moose;
|
|
100 1;
|