39 lines
857 B
Perl
39 lines
857 B
Perl
#!/usr/bin/env perl
|
|
|
|
use strict;
|
|
use warnings;
|
|
|
|
use FindBin;
|
|
|
|
my $usage = "usage: $0 RSEM.isoforms.fpkm\n\n";
|
|
|
|
my $fpkm_file = $ARGV[0] or die $usage;
|
|
|
|
my $Rscript = "$fpkm_file.R";
|
|
open (my $ofh, ">$Rscript");
|
|
print $ofh "source(\"$FindBin::RealBin/R/expression_analysis_lib.R\")\n";
|
|
print $ofh "pdf(\"$fpkm_file.genes_vs_minFPKM.pdf\")\n";
|
|
print $ofh "plot_expressed_gene_counts(\"$fpkm_file\", title=\"expressed transcripts vs. min FPKM\", fpkm_range=seq(0,5,0.01), outfile=\"$fpkm_file.genes_vs_minFPKM.dat\")\n";
|
|
print $ofh "dev.off()\n";
|
|
close $ofh;
|
|
|
|
&process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $Rscript");
|
|
|
|
|
|
exit(0);
|
|
|
|
|
|
####
|
|
sub process_cmd {
|
|
my ($cmd) = @_;
|
|
|
|
print STDERR "CMD: $cmd\n";
|
|
|
|
my $ret = system($cmd);
|
|
if ($ret) {
|
|
die "Error, cmd: $cmd died with ret $ret";
|
|
}
|
|
|
|
return;
|
|
}
|