Mercurial > repos > dereeper > roary_plots
view Roary/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm @ 3:e95344f6dfc5 draft default tip
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author | dereeper |
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date | Fri, 12 Nov 2021 16:32:26 +0000 |
parents | c47a5f61bc9f |
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undef $VERSION; package Bio::Roary::CommandLine::RoaryReorderSpreadsheet; # ABSTRACT: Take in a tree and a spreadsheet and output a reordered spreadsheet =head1 SYNOPSIS Take in a tree and a spreadsheet and output a reordered spreadsheet =cut use Moose; use Getopt::Long qw(GetOptionsFromArray); use Bio::Roary::ReorderSpreadsheet; extends 'Bio::Roary::CommandLine::Common'; has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 ); has 'help' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'tree_file' => ( is => 'rw', isa => 'Str' ); has 'spreadsheet_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' ); has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'reordered_spreadsheet.csv' ); has 'tree_format' => ( is => 'rw', isa => 'Str', default => 'newick' ); has 'search_strategy' => ( is => 'rw', isa => 'Str', default => 'depth' ); has 'sortby' => ( is => 'rw', isa => 'Str', default => 'height'); has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 ); sub BUILD { my ($self) = @_; my ( $output_filename, $tree_file,$search_strategy, $sortby, $tree_format, $spreadsheet_filename,$verbose, $help ); GetOptionsFromArray( $self->args, 'o|output_filename=s' => \$output_filename, 't|tree_file=s' => \$tree_file, 'f|tree_format=s' => \$tree_format, 's|spreadsheet_filename=s' => \$spreadsheet_filename, 'a|search_strategy=s' => \$search_strategy, 'b|sortby=s' => \$sortby, 'v|verbose' => \$verbose, 'h|help' => \$help, ); if ( defined($verbose) ) { $self->verbose($verbose); $self->logger->level(10000); } $self->help($help) if(defined($help)); $self->output_filename($output_filename) if ( defined($output_filename) ); $self->tree_file($tree_file) if ( defined($tree_file) ); $self->tree_format($tree_format) if ( defined($tree_format) ); $self->spreadsheet_filename($spreadsheet_filename) if ( defined($spreadsheet_filename) ); $self->sortby($sortby) if ( defined($sortby) ); $self->search_strategy($search_strategy) if ( defined($search_strategy) ); } sub run { my ($self) = @_; ( defined($self->spreadsheet_filename) && defined($self->tree_file) && ( -e $self->spreadsheet_filename ) && ( -e $self->tree_file ) && ( !$self->help ) ) or die $self->usage_text; ($self->sortby eq "height" || $self->sortby eq "creation" || $self->sortby eq "alpha" || $self->sortby eq "revalpha") or die $self->usage_text; ($self->search_strategy eq "breadth" || $self->search_strategy eq "depth") or die $self->usage_text; my $obj = Bio::Roary::ReorderSpreadsheet->new( tree_file => $self->tree_file, spreadsheet => $self->spreadsheet_filename, output_filename => $self->output_filename, sortby => $self->sortby, search_strategy => $self->search_strategy ); $obj->reorder_spreadsheet(); } sub usage_text { my ($self) = @_; return <<USAGE; Usage: pan_genome_reorder_spreadsheet [options] -t tree.newick Reorder the columns in the gene presence and absence spreadsheet against a phylogenetic tree. Options: -t STR tree filename [] -o STR output filename [reordered_spreadsheet.csv] -f STR tree format (newick/nexus/nhx/svggraph/tabtree/lintree) [newick] -s STR input gene presence and absence spreadsheet [gene_presence_absence.csv] -a STR search strategy (depth/breadth) [depth] -b STR sorting method (height/creation/alpha/revalpha) [height] -v verbose output to STDOUT -h this help message For further info see: http://sanger-pathogens.github.io/Roary/ USAGE } __PACKAGE__->meta->make_immutable; no Moose; 1;