/usr/share/perl5/Genome/Model/Tools/Music/Plot/MutationRelation.pm is in libgenome-model-tools-music-perl 0.04-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | package Genome::Model::Tools::Music::Plot::MutationRelation;
use warnings;
use strict;
use Genome;
use IO::File;
use List::Util qw( sum );
use Carp;
use POSIX qw( WIFEXITED );
our $VERSION = $Genome::Model::Tools::Music::VERSION;
class Genome::Model::Tools::Music::Plot::MutationRelation {
is => 'Command::V2',
has_input => [
input_matrix => { is => 'String', doc => "A gene/sample matrix generated by the mutation-relation tool" },
output_pdf => { is => 'String', doc => "An output pdf file to draw the plot to" },
],
has_optional_input => [
skip_zero_mut_samples => { is => 'Boolean', doc => "Don't plot samples that have no mutations on any gene being plotted", default => 1 },
genes_to_plot => { is => 'String', doc => "Comma-separated list of genes to plot (example: DNMT3A,NPM1)" },
plot_genes_in_order_listed => { is => 'Boolean', doc => "Plot the genes in the order that they're listed. Default is to plot them in descending order by number of mutations", default => 0 },
],
doc => "Makes plots for results from the mutation-relation tool",
};
sub help_detail {
return <<HELP;
Given a matrix generated using "music mutation-relation --mutation-matrix-file", this
tool will generate a plot that highlights mutual exclusivity or concurrence between the mutation
status of a predefined set of genes.
HELP
}
#########################################################################
sub execute {
my $self = shift;
my $input_matrix = $self->input_matrix;
my $output_pdf = $self->output_pdf;
my $skip_zero_mut_samples = $self->skip_zero_mut_samples;
my $genes_to_plot = $self->genes_to_plot;
my $plot_genes_in_order_listed = $self->plot_genes_in_order_listed;
# Load the gene names from the matrix
my $headFh = IO::File->new( $input_matrix );
my @cols = split( /\t/, $headFh->getline );
# Create a hash of the gene names, which associates each with an R-friendly name
my %genes_in_matrix = map{chomp; my $t = $_; s/\W/_/g; ( $t, $_ )} splice( @cols, 1 );
$headFh->close;
# Discard any user-specified genes that are not in the input matrix
# being sure to preserve the order of the genes in the input
if( defined $genes_to_plot ) {
my %genes = map{($_,1)} split( /,/, $genes_to_plot );
foreach my $gene ( keys %genes ) {
unless( defined $genes_in_matrix{$gene} ) {
warn "Skipping gene $gene which is not seen in the provided input-matrix\n";
delete $genes{$gene};
}
}
#preserve the order of genes in the input
my @glist = split(",",$genes_to_plot);
my @finalList;
foreach my $g (@glist){
if(defined($genes{$g})){
push(@finalList, $g)
}
}
$genes_to_plot = join(",",@finalList);
}
# If user didn't specify genes-to-plot, then plot every gene in the input-matrix
else {
$genes_to_plot = join( ",", values %genes_in_matrix );
}
# Create a temporary mutation matrix with R-friendly gene names
my $tmp_matrix = Genome::Sys->create_temp_file_path;
( $tmp_matrix ) or die "Couldn't create a temp file. $!";
my $inFh = IO::File->new( $input_matrix );
my $outFh = IO::File->new( $tmp_matrix, ">" );
while( my $line = $inFh->getline ) {
chomp( $line );
my @cols = split( /\t/, $line );
if( $line =~ m/^Sample\t/ ) { # Handle the header line
$outFh->print( join( "\t", $cols[0], map{$genes_in_matrix{$_}}@cols[1..$#cols] ) . "\n" );
}
elsif( !$skip_zero_mut_samples || sum( @cols[1..$#cols] ) > 0 ) {
$outFh->print( join( "\t", @cols ) . "\n" );
}
}
$outFh->close;
$inFh->close;
# Call R to create a plot for the user-specified genes
my $plot_cmd = "R --slave --args < " . __FILE__ . ".R $tmp_matrix $genes_to_plot $output_pdf $plot_genes_in_order_listed";
WIFEXITED( system $plot_cmd ) or croak "Couldn't run: $plot_cmd ($?)";
return 1;
}
1;
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