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#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Cwd;
my $usage = "usage: $0 genome_fa_files.list\n\n";
my $genome_fa_files = $ARGV[0] or die $usage;
my $workdir = cwd();
open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
while (<$fh>) {
chomp;
my $genome_file = $_;
my $outdir = dirname($genome_file);
if ($outdir !~ /^\./) {
$outdir = "$workdir/$outdir";
}
my $cmd = "$ENV{TRINITY_HOME}/Trinity --seqType fa --single $outdir/simul.reads.fa --CPU 1 --max_memory 1G --output $outdir/trinity_WITH_LR_outdir --full_cleanup --long_reads $outdir/simul.transcriptome.cdnas --trinity_complete";
#&process_cmd($cmd);
print "$cmd\n";
}
exit(0);
####
sub process_cmd {
my ($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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