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|
#!/usr/bin/env perl
use strict;
use warnings;
use List::Util qw(shuffle);
my $usage = "usage: $0 counts.matrix num_reads_sample\n\n";
my $matrix_file = $ARGV[0] or die $usage;
my $num_reads_to_sample = $ARGV[1] or die $usage;
main: {
print STDERR "-parsing matrix: $matrix_file\n";
my %matrix_in = &parse_matrix($matrix_file); # matrix{sample}->{gene} = count;
my %matrix_adj; # matrix{gene}->{sample} = count;
my @samples;
foreach my $sample (keys %matrix_in) {
print STDERR "-sampling reads for sample: $sample\n";
my $gene_counts_href = $matrix_in{$sample};
my $sum_counts = &sum(values %$gene_counts_href);
if ($sum_counts < $num_reads_to_sample) {
print STDERR "WARNING: sample $sample only has $sum_counts reads, less than $num_reads_to_sample to sample, skipping it.\n";
next;
}
push (@samples, $sample);
my @sampled_reads = &sample_from_read_counts($gene_counts_href, $num_reads_to_sample);
foreach my $read (@sampled_reads) {
$matrix_adj{$read}->{$sample}++;
}
}
print STDERR "-outputting new matrix containing downsampled reads.\n";
## output new matrix.
print "\t" . join("\t", @samples) . "\n";
foreach my $gene (keys %matrix_adj) {
print $gene;
foreach my $sample (@samples) {
my $count = $matrix_adj{$gene}->{$sample} || 0;
print "\t$count";
}
print "\n";
}
exit(0);
}
####
sub sample_from_read_counts {
my ($gene_counts_href, $num_reads_to_sample) = @_;
my @reads;
foreach my $gene (keys %$gene_counts_href) {
my $count = int($gene_counts_href->{$gene} + 0.5);
for (my $i = 1; $i <= $count; $i++) {
push (@reads, $gene);
}
}
if (scalar @reads < $num_reads_to_sample) {
die "Error, only captured " . scalar(@reads) . ", less than $num_reads_to_sample.... shouldn't happen... ";
}
@reads = shuffle @reads;
@reads = @reads[0..($num_reads_to_sample-1)];
return(@reads);
}
####
sub sum {
my @vals = @_;
my $sum = 0;
foreach my $val (@vals) {
$sum += $val;
}
return($sum);
}
####
sub parse_matrix {
my ($matrix_file) = @_;
open (my $fh, $matrix_file) or die "Error, cannot open file $matrix_file";
my $header = <$fh>;
$header =~ s/^\s+//;
chomp $header;
my @fields = split(/\t/, $header);
my $adj_fields_flag = 0;
my %matrix;
while (<$fh>) {
chomp;
my @vals = split(/\t/);
unless ($adj_fields_flag) {
if (scalar(@vals) == scalar(@fields) + 1) {
unshift(@fields, ""); # add a column for the gene name
}
unless (scalar @vals == scalar @fields) {
die "Error, number of column headers is inconsistent with number of data fields.";
}
$adj_fields_flag = 1;
}
my $gene = $vals[0];
for (my $i = 1; $i <= $#fields; $i++) {
my $field = $fields[$i];
my $val = $vals[$i];
$matrix{$field}->{$gene} = $val;
}
}
close $fh;
return(%matrix);
}
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