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#!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
my $usage = "usage: $0 info_files.list.txt output_basedir [eval cmds]\n\n";
my $files_listing_file = $ARGV[0] or die $usage;
my $output_basedir = $ARGV[1] or die $usage;
shift @ARGV;
shift @ARGV;
main: {
my @files = `cat $files_listing_file`;
chomp @files;
my $eval_script = "/usr/lib/trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.sh";
my $basedir = cwd();
unless ($output_basedir =~ /^\//) {
$output_basedir = "$basedir/$output_basedir";
}
foreach my $file (@files) {
my $line = `cat $file`;
chomp $line;
my ($refseq_fa_file, $left_fa, $right_fa) = split(/\t/, $line);
my @pts = split(/\//, $refseq_fa_file);
my $gene_name = $pts[-2];
my $cmd = "$eval_script -R $refseq_fa_file --left $left_fa --right $right_fa -O $output_basedir/$gene_name @ARGV";
print "$cmd\n";
}
exit(0);
}
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