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#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "usage: $0 sample_avg_expr.matrix edgeR_directory/ [FDR=0.05]\n\n";
my $sample_expr_matrix = $ARGV[0] or die $usage;
my $DE_dir = $ARGV[1] or die $usage;
my $MAX_FDR = $ARGV[2];
unless (defined $MAX_FDR) {
$MAX_FDR = 0.05;
}
my @DE_result_files = <$DE_dir/*.DE_results>;
unless (@DE_result_files) {
die "Error, cannot find \*.DE_results files at $DE_dir ";
}
main: {
my %gene_to_sample_expr_val = &parse_expression_matrix($sample_expr_matrix);
print join("\t", "#feature", "sample_A", "sample_B", "log2(exprA)", "log2(exprB)", "logFC", "FDR") . "\n";
foreach my $DE_result_file (@DE_result_files) {
print STDERR "-processing DE file: $DE_result_file\n";
$DE_result_file =~ /\.([^\.\/]+)_vs_([^\.\/]+).[^\.]+.DE_results/ or die "Error, cannot parse filename: $DE_result_file";
my $sample_A = $1;
my $sample_B = $2;
open (my $fh, $DE_result_file) or die $!;
my $header = <$fh>;
chomp $header;
my @header_fields = split(/\t/, $header);
my $FDR_field = undef;
my $line_counter = 0;
while(<$fh>) {
$line_counter++;
chomp;
my @x = split(/\t/);
# match up header with data fields.
if ($line_counter == 1) {
if (scalar(@header_fields) == scalar(@x) -1) {
unshift(@header_fields, 'id');
}
elsif (scalar(@header_fields) != scalar(@x)) {
die "Error, disconnect between header line and data line, number of fields are unequal and header isn't one short:\n"
. "header: @header_fields\n"
. "line: @x\n";
}
for (my $i = 0; $i <= $#header_fields; $i++) {
if ($header_fields[$i] eq 'FDR') {
$FDR_field = $i;
}
}
unless ($FDR_field) {
die "Error, couldn't identify column corresponding to FDR";
}
}
my $feature = $x[0];
my $feature_expr = $gene_to_sample_expr_val{$feature};
unless (defined $feature_expr) {
die "Error, no expression values stored for [$feature] ";
}
my $FDR = $x[$FDR_field];
if ($FDR <= $MAX_FDR) {
my $expr_sample_A = $feature_expr->{$sample_A};
my $expr_sample_B = $feature_expr->{$sample_B};
unless (defined $expr_sample_A && defined $expr_sample_B) {
die "Error, no expr value for feature: $feature, $sample_A [$expr_sample_A] or $sample_B [$expr_sample_B] " . Dumper($gene_to_sample_expr_val{$feature});
}
my $log_expr_sample_A = log($expr_sample_A+1)/log(2);
my $log_expr_sample_B = log($expr_sample_B+1)/log(2);
my $log_FC = sprintf("%.2f", $log_expr_sample_A - $log_expr_sample_B);
print join("\t", $feature, $sample_A, $sample_B, $log_expr_sample_A, $log_expr_sample_B, $log_FC, $FDR) . "\n";
}
}
}
print STDERR "\nDone\n\n";
exit(0);
}
####
sub parse_expression_matrix {
my ($expr_matrix_file) = @_;
print STDERR "\nReading matrix: $expr_matrix_file ... ";
my $cmd = "wc -l $expr_matrix_file ";
my $num_lines = `$cmd`;
if ($?) {
die "Error, cmd; $cmd died with ret $?";
}
$num_lines =~ /(\d+)/;
$num_lines = $1 or die "Error, cannot count number of lines from: $num_lines, cmd: $cmd";
print STDERR " $num_lines rows of matrix detected.\n\n";
my %gene_to_sample_expr_val;
open (my $fh, $expr_matrix_file) or die "Error, cannot open file $expr_matrix_file";
my $header = <$fh>;
chomp $header;
$header =~ s/^\s+//;
my @sample_names = split(/\t/, $header);
my $counter = 0;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $feature_name = shift @x;
#unless ($feature_name eq "c1088792_g2_i5^sp|Q06441|TSP4_XENLA^COMP^sigP") { next; }
unless (scalar @x == scalar @sample_names) {
die "Error, number of samples: " . scalar (@sample_names) . " doesn't match number of values read: " . scalar(@x) . " ";
}
for (my $i = 0; $i <= $#sample_names; $i++) {
my $sample = $sample_names[$i];
my $val = $x[$i];
$gene_to_sample_expr_val{$feature_name}->{$sample} = $val;
}
$counter++;
if ($counter % 10000 == 0) {
my $pct_done = sprintf("%.2f", $counter/$num_lines * 100);
print STDERR "\r[$pct_done %] matrix read. ";
}
#if ($counter > 10) { last; } # debug
}
close $fh;
print STDERR "\n\nDone reading matrix.\n";
#print Dumper(\%gene_to_sample_expr_val);
return(%gene_to_sample_expr_val);
}
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