Genome-Model-Tools-Music
view release on metacpan or search on metacpan
lib/Genome/Model/Tools/Music/Survival.pm view on Meta::CPAN
package Genome::Model::Tools::Music::Survival;
use warnings;
use strict;
use Carp;
use Genome;
use IO::File;
use POSIX qw( WIFEXITED );
our $VERSION = $Genome::Model::Tools::Music::VERSION;
class Genome::Model::Tools::Music::Survival {
is => 'Genome::Model::Tools::Music::Base',
has_input => [
bam_list => {
is => 'Text',
doc => "List of sample names to be included in the analysis. (See Description)",
},
maf_file => {
is => 'Text', is_optional => 1,
doc => "List of mutations in MAF format",
},
output_dir => {
is => 'Text', is_output => 1,
doc => "Directory where output files will be written",
},
genetic_data_type => {
is => 'Text', is_optional => 1, default => "gene",
doc => "Correlate clinical data to \"gene\" or \"variant\" level data",
},
numeric_clinical_data_file => {
is => 'Text', is_optional => 1,
doc => "Table of samples (y) vs. numeric clinical data category (x)",
},
categorical_clinical_data_file => {
is => 'Text', is_optional => 1,
doc => "Table of samples (y) vs. categorical clinical data category (x)",
},
glm_clinical_data_file => {
is => 'Text', is_optional => 1,
doc => "Clinical traits, mutational profiles, other mixed clinical data (See DESCRIPTION).",
},
phenotypes_to_include => {
is => 'Text', is_optional => 1,
doc => "Include only these genes and/or phenotypes in the anlaysis. (COMMA-DELIMITED)",
},
legend_placement => {
is => 'Text', is_optional => 1, default => 'bottomleft',
doc => "Choose one of 'bottomleft', 'topleft', 'topright', or 'bottomright'.",
},
skip_non_coding => {
is => 'Boolean', is_optional => 1, default => 1,
doc => "Skip non-coding mutations from the provided MAF file",
},
skip_silent => {
is => 'Boolean', is_optional => 1, default => 1,
doc => "Skip silent mutations from the provided MAF file",
},
],
doc => "Create survival plots and P-values for clinical and mutational phenotypes.",
};
sub help_synopsis {
return <<HELP
... music survival \\
--bam-list /path/myBamList.tsv \\
--maf-file /path/myMAF.tsv \\
--numeric-clinical-data-file /path/myNumericData.tsv \\
--categorical-clinical-data-file /path/myClassData.tsv \\
--output-dir /path/output_directory
... music survival \\
--bam-list /path/myBamList.tsv \\
--maf-file /path/myMAF.tsv \\
--glm-clinical-data-file /path/myGLMClinicalData.tsv \\
--output-dir /path/output_directory
... music survival \\
--bam-list /path/myBamList.tsv \\
--maf-file /path/myMAF.tsv \\
--genetic-data-type 'gene' \\
--glm-clinical-data-file /path/myGlmClinicalData.tsv \\
--phenotypes-to-include 'Race,Gender,TP53' \\
--output-dir /path/output_directory
HELP
}
sub help_detail {
return <<HELP
This command performs survival analysis and plots survival curves for mutational data, as well as any clinical traits of interest as specified via the --phenotypes-to-include input parameter. The analyses performed include the Kaplan-Meier estimator ...
All clinical data files are searched for the required (case insensitive) "vital_status" and "days_to_last_followup" columns which are paired to phenotypes via sample IDs for the survival analysis. The first column of all clinical data files MUST cont...
Here are some general guildelines for creating clinical data input files:
=over 4
=item * Headers are required.
=item * The first column of each clinical data file must contain sample IDs which match those in both the --bam-list and the MAF variant list (in the MAF, this is the Tumor_Sample_Barcode column, specifically).
=item * In at least one of the clinical data files input, columns with headers "vital_status" and "days_to_last_followup" (case insensitive) must exist. "vital_status" must be delineated by 1's and 0's, where 0 denotes 'living', and 1 denotes 'deceas...
=back
Note that all input files must be tab-separated.
HELP
}
sub _additional_help_sections {
return (
"ARGUMENTS",
<<EOS
=over 4
=item --bam-list
=over 8
=item Provide a file containing sample names and normal/tumor BAM locations for each. Use the tab-
delimited format [sample_name normal_bam tumor_bam] per line. This tool only needs sample_name,
so all other columns can be skipped. The sample_name must be the same as the tumor sample names
used in the MAF file (16th column, with the header Tumor_Sample_Barcode).
=back
=back
EOS
);
}
sub _doc_authors {
return <<EOS
Nathan D. Dees, Ph.D.
Qunyuan Zhang, Ph.D.
EOS
}
sub execute {
# parse input arguments
my $self = shift;
my $bam_list = $self->bam_list;
my $genetic_data_type = $self->genetic_data_type;
my $legend_placement = $self->legend_placement;
# handle phenotype inclusions
my @phenotypes_to_include;
my @clinical_phenotypes_to_include;
my @mutated_genes_to_include;
if ($self->phenotypes_to_include) { @phenotypes_to_include = split /,/,$self->phenotypes_to_include; }
# check genetic data type
unless ($genetic_data_type =~ /^gene|variant$/i) {
$self->error_message("Please enter either \"gene\" or \"variant\" for the --genetic-data-type parameter.");
return;
}
# load clinical data and analysis types
my %clinical_data;
if ($self->numeric_clinical_data_file) {
$clinical_data{'numeric'} = $self->numeric_clinical_data_file;
}
if ($self->categorical_clinical_data_file) {
$clinical_data{'categ'} = $self->categorical_clinical_data_file;
}
if ($self->glm_clinical_data_file) {
$clinical_data{'glm'} = $self->glm_clinical_data_file;
}
# create array of all sample names possibly included from clinical data and MAF
my @all_sample_names; # names of all the samples, no matter if they are mutated or not
my $sampleFh = IO::File->new( $bam_list ) or die "Couldn't open $bam_list. $!\n";
while( my $line = $sampleFh->getline )
{
next if ( $line =~ m/^#/ );
chomp( $line );
my ( $sample ) = split( /\t/, $line );
push( @all_sample_names, $sample );
}
$sampleFh->close;
# loop through clinical data files and assemble survival data hash (vital_status and days_to_last_followup required);
my %survival_data;
my $vital_status_flag = 0;
my $days_to_last_follow_flag = 0;
for my $clin_file (keys %clinical_data) {
#check filehandle
my $clin_fh = new IO::File $clinical_data{$clin_file},"r";
unless ($clin_fh) {
$self->error_message("Failed to open $clinical_data{$clin_file} for reading: $!");
return;
}
#initiate variables to hold column info
my %phenotypes_to_print;
my $vital_status_col = 0;
my $days_to_last_follow_col = 0;
#parse header and record column locations for needed data
my $header = $clin_fh->getline;
my @header_fields = split /\t/,$header;
for (my $i = 1; $i <= $#header_fields; $i++) { #sample ID should be in first column of file
lib/Genome/Model/Tools/Music/Survival.pm view on Meta::CPAN
$self->error_message('Clinical data does not seem to contain a column labeled "vital_status".');
return;
}
unless ($days_to_last_follow_flag) {
$self->error_message('Clnical data does not seem to contain a column labeled "days_to_last_followup".');
return;
}
# create temporary files for R command
my $survival_data_file = Genome::Sys->create_temp_file_path();
my $mutation_matrix = Genome::Sys->create_temp_file_path();
# print survival data (temp file)
my $surv_fh = new IO::File $survival_data_file,"w" or die "Couldn't open survival data filehandle.";
print $surv_fh join("\t","Sample","Days_To_Last_Followup","Vital_Status");
if (@clinical_phenotypes_to_include) { print $surv_fh "\t" . join("\t",@clinical_phenotypes_to_include); }
print $surv_fh "\n";
for my $sample (keys %survival_data) {
unless (exists $survival_data{$sample}{'days'}) { $survival_data{$sample}{'days'} = "NA"; }
unless (exists $survival_data{$sample}{'vital_status'}) { $survival_data{$sample}{'vital_status'} = "NA"; }
print $surv_fh join("\t",$sample,$survival_data{$sample}{'days'},$survival_data{$sample}{'vital_status'});
for my $pheno (@clinical_phenotypes_to_include) {
unless (exists $survival_data{$sample}{$pheno}) { $survival_data{$sample}{$pheno} = "NA"; }
print $surv_fh "\t" . $survival_data{$sample}{$pheno};
}
print $surv_fh "\n";
}
$surv_fh->close;
# find if any of the "phenotypes_to_include" are genes, and if so, limit the MAF mutation matrix to those genes
my %clinical_pheno_to_include;
@clinical_pheno_to_include{@clinical_phenotypes_to_include} = ();
for my $item (@phenotypes_to_include) {
push @mutated_genes_to_include,$item unless exists $clinical_pheno_to_include{$item};
}
my $mutated_genes_to_include = \@mutated_genes_to_include;
# create mutation matrix file
if( $genetic_data_type =~ /^gene$/i ) {
$self->create_sample_gene_matrix_gene( $mutation_matrix, $mutated_genes_to_include, @all_sample_names );
}
elsif( $genetic_data_type =~ /^variant$/i ) {
$self->create_sample_gene_matrix_variant( $mutation_matrix, $mutated_genes_to_include, @all_sample_names );
}
else {
$self->error_message( "Please enter either \"gene\" or \"variant\" for the --genetic-data-type parameter." );
return;
}
# check and prepare output directory
my $output_dir = $self->output_dir . "/";
unless (-e $output_dir) {
$self->status_message("Creating output directory: $output_dir...");
unless(mkdir $output_dir) {
$self->error_message("Failed to create output directory: $!");
return;
}
}
# set up R command
my $R_cmd = "R --slave --args < " . __FILE__ . ".R " . join( " ", $survival_data_file, $mutation_matrix, $legend_placement, $output_dir );
print "R_cmd:\n$R_cmd\n";
#run R command
WIFEXITED( system $R_cmd ) or croak "Couldn't run: $R_cmd ($?)";
return(1);
}
sub create_sample_gene_matrix_gene {
my ( $self, $mutation_matrix, $mutated_genes_to_include, @all_sample_names ) = @_;
#create hash of mutations from the MAF file
my ( %mutations, %all_genes );
#parse the MAF file and fill up the mutation status hashes
my $maf_fh = IO::File->new( $self->maf_file ) or die "Couldn't open MAF file!\n";
while( my $line = $maf_fh->getline ) {
next if( $line =~ m/^(#|Hugo_Symbol)/ );
chomp $line;
my @cols = split( /\t/, $line );
my ( $gene, $mutation_class, $sample ) = @cols[0,8,15];
#check that the mutation class is valid
if( $mutation_class !~ m/^(Missense_Mutation|Nonsense_Mutation|Nonstop_Mutation|Splice_Site|Translation_Start_Site|Frame_Shift_Del|Frame_Shift_Ins|In_Frame_Del|In_Frame_Ins|Silent|Intron|RNA|3'Flank|3'UTR|5'Flank|5'UTR|IGR|Targeted_Region|De_...
$self->error_message( "Unrecognized Variant_Classification \"$mutation_class\" in MAF file for gene $gene\nPlease use TCGA MAF v2.3.\n" );
return;
}
#check to see if this gene is on the list (if there is a list at all)
if( defined @{$mutated_genes_to_include} ) {
next unless( scalar grep { m/^$gene$/ } @{$mutated_genes_to_include} );
}
# If user wants, skip Silent mutations, or those in Introns, RNA, UTRs, Flanks, IGRs, or the ubiquitous Targeted_Region
if(( $self->skip_non_coding && $mutation_class =~ m/^(Intron|RNA|3'Flank|3'UTR|5'Flank|5'UTR|IGR|Targeted_Region)$/ ) ||
( $self->skip_silent && $mutation_class =~ m/^Silent$/ )) {
print "Skipping $mutation_class mutation in gene $gene.\n";
next;
}
$all_genes{$gene}++;
$mutations{$sample}{$gene}++;
}
$maf_fh->close;
#sort @all_genes for consistency in header and loops
my @all_genes = sort keys %all_genes;
#write the input matrix for R code to a temp file
my $matrix_fh = new IO::File $mutation_matrix,"w" or die "Failed to create matrix file $mutation_matrix!: $!";
#print input matrix file header
my $header = join( "\t", "Sample", @all_genes );
$matrix_fh->print( "$header\n" );
#print mutation relation input matrix
for my $sample ( sort @all_sample_names ) {
$matrix_fh->print( $sample );
for my $gene ( @all_genes ) {
( run in 0.565 second using v1.01-cache-2.11-cpan-39bf76dae61 )