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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 edgeR_dir\n\n";
my $edgeR_dir = $ARGV[0] or die $usage;
unless (-d $edgeR_dir) {
die "Error, require a directory name for the parameter.\n\n$usage\n";
}
my ($fpkm_matrix_file) = <$edgeR_dir/*FPKM>;
unless ($fpkm_matrix_file) {
die "Error, cannot locate the FPKM matrix file at $edgeR_dir";
}
for my $fold_change (1..8) {
for my $pvalue (2..10) {
my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix $fpkm_matrix_file -C $fold_change -P 1e-$pvalue";
&process_cmd($cmd);
}
}
exit(0);
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, CMD: $cmd died with ret $ret";
}
return;
}
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