20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,92 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Carp;
+use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
+
+my $help_flag;
+
+my $CPU = 4;
+my $output_dir = "DetonateData";
+
+my $species_opts = "mouse|human|fission_yeast";
+
+my $usage = <<__EOUSAGE__;
+
+#######################################################################################
+#
+#  (note, must set env var DETONATE_HOME to installation directory of DETONATE software)
+#
+#  --reads <string>       if paired-end, list as comma-delimited:  "left.fq,right.fq"
+#
+#  --target <string>      target fasta file (eg. Trinity.fasta)
+#
+#  --frag_len <string>    frag length. If SE data, it's the read length.
+#
+#  --species <string>     $species_opts  (param files provided at: rsem-eval/true_transcript_length_distribution/)
+#
+#  optional:
+#
+#  --SS_lib_type <string>  R, F, RF, or FR
+#
+#  --threads <int>        number of threads to use in multi-threading (default: $CPU)
+#
+#  --output_dir <string>  default: $output_dir
+#
+########################################################################################
+
+
+__EOUSAGE__
+
+    ;
+
+
+my $reads;
+my $target;
+my $frag_len;
+my $SS_lib_type;
+my $species;
+
+&GetOptions ( 'h' => \$help_flag,
+              
+              'reads=s' => \$reads,
+              'target=s' => \$target,
+              'frag_len=i' => \$frag_len,
+              'SS_lib_type=s' => \$SS_lib_type,
+              'threads=i' => \$CPU,
+              'output_dir=s' => \$output_dir,
+              'species=s' => \$species,
+    );
+
+
+unless ($reads && $target && $frag_len && $species) {
+    die $usage;
+}
+
+
+main: {
+
+    my $detonate_home_dir = $ENV{DETONATE_HOME} or die "Error, must set env var DETONATE_HOME to its installation directory";
+
+    unless (defined($species) && $species =~ /$species_opts/) {
+        die "Error, species $species not supported, only $species_opts";
+    }
+
+    my $cmd = "$detonate_home_dir/rsem-eval/rsem-eval-calculate-score -p $CPU "
+     . " --transcript-length-parameters $detonate_home_dir/rsem-eval/true_transcript_length_distribution/$species.txt "
+     . " $reads $target $output_dir $frag_len ";
+
+    my $ret = system($cmd);
+
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+    
+    else {
+        print STDERR "Done.\n";
+    }
+    exit(0);
+    
+}