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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fasta [require_proper_pairs_flag] [include_volcano_spread]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $require_proper_pairs_flag = $ARGV[1] or die $usage;
my $include_volcano_spread = $ARGV[2] or die $usage;
main: {
my $sim_out_dir = "sim_data";
unless (-d $sim_out_dir) {
mkdir $sim_out_dir or die $!;
}
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
my $outdir = $acc;
$outdir =~ s/\W/_/g;
mkdir ("$sim_out_dir/$outdir") or die $!;
my $template_file = "$sim_out_dir/$outdir/$outdir.template.fa";
open (my $ofh, ">$template_file") or die "Error, cannot write to $template_file";
print $ofh ">$acc\n$sequence\n";
close $ofh;
my $outfile = "$sim_out_dir/$outdir/$outdir.reads.fa";
my $cmd = "/usr/lib/trinityrnaseq/util/misc/simulate_illuminaPE_from_transcripts.pl --transcripts $template_file --out_prefix $template_file";
if ($require_proper_pairs_flag) {
$cmd .= " --require_proper_pairs";
}
if ($include_volcano_spread) {
$cmd .= " --include_volcano_spread";
}
&process_cmd($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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