EukHighConfidenceFilter.in

@@ -402,7 +402,14 @@ sub euk_anticodon_filter
 	my ($ac_count, $tRNA) = @_;
 	my $tag = "";
 	
-	if (!defined $euk_aa_list{$tRNA->anticodon()} and !$tRNA->is_pseudo())
+	if (!$tRNA->is_pseudo())
+	{
+		if ($tRNA->isotype() eq "Sup")
+		{
+			$tag = "unexpected anticodon";
+			$tRNA_counts{ac_filter}++;
+		}		
+		elsif (!defined $euk_aa_list{$tRNA->anticodon()})
 		{
 			my $alt_anticodon = $tRNA->anticodon();
 			if (substr($tRNA->anticodon(), 0, 1) eq "A")
@@ -423,6 +430,7 @@ sub euk_anticodon_filter
 				$tRNA_counts{ac_filter}++;
 			}
 		}
+	}
 	
 	return $tag;
 }
@@ -762,7 +770,7 @@ sub write_out_file
 				elsif (!$tRNA->is_pseudo())
 				{
 					$include = 1;
-					if ($columns[$header{note}] =~ /IPD/)
+					if ($columns[$header{note}] =~ /IPD/ and $columns[$header{isotype}] ne "Sup")
 					{
 						$tRNA_counts{iso_filter}++;
 						$tag = "isotype mismatch";

debian/changelog

-trnascan-se (2.0.0-4) UNRELEASED; urgency=medium
+trnascan-se (2.0.3-2) UNRELEASED; urgency=medium
+
+  * Added a few autogenerated files to be excluded for
+    d/copyright.
+
+    
+
+ -- Steffen Moeller <moeller@debian.org>  Sat, 03 Aug 2019 15:34:03 +0200
+
+trnascan-se (2.0.3-1) unstable; urgency=medium
+
+  * Team upload.
 
   [ Andreas Tille ]
   * Upstream agreed to GPL the code here:
@@ -8,6 +19,11 @@ trnascan-se (2.0.0-4) UNRELEASED; urgency=medium
   * Build-Depend on infernal to block the package being built on
     architectures where it's not available
 
+  [ Steffen Moeller ]
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+
  -- Andreas Tille <tille@debian.org>  Tue, 25 Sep 2018 07:38:08 +0200
 
 trnascan-se (2.0.0-3) unstable; urgency=medium

debian/compat

-11

debian/control

@@ -4,9 +4,9 @@ Uploaders: Afif Elghraoui <afif@debian.org>
 Section: non-free/science
 XS-Autobuild: no
 Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper-compat (= 12),
                infernal
-Standards-Version: 4.2.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/trnascan-se
 Vcs-Git: https://salsa.debian.org/med-team/trnascan-se.git
 Homepage: http://lowelab.ucsc.edu/tRNAscan-SE

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: tRNAscan-SE
 Upstream-Contact: Todd Lowe <lowe@soe.ucsc.edu>
 Source: http://lowelab.ucsc.edu/software/
@@ -6,6 +6,14 @@ Disclaimer: This package is not part of Debian because of the non-free
  license of the single file src/trnascan.c.  An attempt to get a free
  license for the whole code was made here:
    https://lists.debian.org/debian-med/2018/08/msg00013.html
+Files-Excluded:
+ Makefile.in
+ aclocal.m4
+ configure
+ depcomp
+ install-sh
+ missing
+
 
 Files: *
 Copyright:

debian/watch

 version=4
 
-opts="uversionmangle=s/rc/~rc/i" \
+opts="uversionmangle=s/rc/~rc/i,repack,compression=gz" \
 http://trna.ucsc.edu/software/trnascan-se-(.*)\.tar\.gz

lib/tRNAscanSE/ArraytRNA.pm

@@ -341,17 +341,7 @@ sub sort_by_tRNAscanid
 
 sub sort_by_gtrnadb_id
 {
-	my $a_code = 0;
-	my $b_code = 0;
-	if ($a->gtrnadb_id() !~ /^tRNA/)
-	{
-		$a_code = 1;
-	}
-	if ($b->gtrnadb_id() !~ /^tRNA/)
-	{
-		$b_code = 1;
-	}	
-    return ($a_code <=> $b_code || $a->gtrnadb_id() cmp $b->gtrnadb_id()); 
+    return ($a->gtrnadb_id() cmp $b->gtrnadb_id()); 
 }
 
 sub sort_by_extdb_id

lib/tRNAscanSE/CM.pm

@@ -79,7 +79,7 @@ sub initialize
     $self->{cmsearch_bin} = "cmsearch";
     $self->{cmscan_bin} = "cmscan";
 
-    $self->{infernal_thread} = 0;
+    $self->{infernal_thread} = -1;
     
     $self->{tab_results} = +[];
 }
@@ -1242,6 +1242,14 @@ sub fix_fMet
                 {
                     $trna->end($trna->end() + 1);
                 }
+                my @ar_ac_pos = $trna->ar_ac_pos();
+                if (scalar(@ar_ac_pos) > 0)
+                {
+					$ar_ac_pos[0]->{rel_start} += 1;
+                    $ar_ac_pos[0]->{rel_end} += 1;
+                    $trna->ar_ac_pos(@ar_ac_pos);
+				}
+				
                 $rescore = 1;
             }
             elsif (substr($trna->ss(), 0, 4) eq ".>.>" and substr($trna->seq(), 0, 2) eq "CG")
@@ -1267,6 +1275,13 @@ sub fix_fMet
                     {
                         $trna->end($trna->end() - 1);
                     }
+                    my @ar_ac_pos = $trna->ar_ac_pos();
+                    if (scalar(@ar_ac_pos) > 0)
+                    {
+                        $ar_ac_pos[0]->{rel_start} -= 1;
+                        $ar_ac_pos[0]->{rel_end} -= 1;
+                        $trna->ar_ac_pos(@ar_ac_pos);
+                    }
                     $rescore = 1;
 				}				
             }
@@ -1310,6 +1325,16 @@ sub fix_His
 			$trna->ss(substr($trna->ss(), 1, 3).">".substr($trna->ss(), 5, length($trna->ss())-11)."<".substr($trna->ss(), length($trna->ss())-5, 3).".");
             $trna->start($trna->start() + 1);
             $trna->end($trna->end() - 1);
+            my @ar_ac_pos = $trna->ar_ac_pos();
+            if (scalar(@ar_ac_pos) > 0)
+            {
+                for (my $i = 0; $i < scalar(@ar_ac_pos); $i++)
+                {
+                    $ar_ac_pos[$i]->{rel_start} -= 1;
+                    $ar_ac_pos[$i]->{rel_end} -= 1;
+                }
+                $trna->ar_ac_pos(@ar_ac_pos);
+            }
             $self->rescore_tRNA($global_vars, $trna, $trna);
 		}
 	}
@@ -2281,7 +2306,7 @@ sub exec_cmscan
     {
         $cm_options = "-g --nohmm --notrunc";
     }
-    if ($self->{infernal_thread} != 0)
+    if ($self->{infernal_thread} != -1)
     {
 		$cm_options .= " --cpu ".$self->{infernal_thread};
 	}
@@ -2341,7 +2366,7 @@ sub exec_cmsearch
 			$cm_options .= " -T ".$score_cutoff;
 		}
 	}
-    if ($self->{infernal_thread} != 0)
+    if ($self->{infernal_thread} != -1)
     {
 		$cm_options .= " --cpu ".$self->{infernal_thread};
 	}

lib/tRNAscanSE/ScanResult.pm

@@ -312,6 +312,19 @@ sub output_tRNA
 			{
 				$tRNA->isotype($model);
 			}
+			elsif ($tRNA->isotype() eq "Met" and $type eq "cyto" and $model ne "Met" and $model ne "iMet" and $model ne "fMet")
+			{
+				$tRNA->sort_multi_models("model");
+				my ($met_iso_model, $met_iso_score, $met_iso_ss) = $tRNA->get_model_hit("cyto", $tRNA->isotype());
+				my ($ile2_iso_model, $ile2_iso_score, $ile2_iso_ss) = $tRNA->get_model_hit("cyto", "Ile2");
+				if ($ile2_iso_score > 0 and $met_iso_score > 0)
+				{
+					if (($score - $ile2_iso_score) <= 5 and ($ile2_iso_score - $met_iso_score) >= 5 and $tRNA->score() > 50)
+					{
+						$tRNA->isotype("Ile2");
+					}
+				}
+			}
 			
 			if (!$opts->results_to_stdout())
 			{
@@ -1001,6 +1014,20 @@ sub write_bed
 						$tRNA->isotype($model);
 						$tRNA->tRNAscan_id($tRNA->seqname().".tRNA".$tRNA->id()."-".$tRNA->isotype().$tRNA->anticodon());
 					}
+					elsif ($tRNA->isotype() eq "Met" and $type eq "cyto" and $model ne "Met" and $model ne "iMet" and $model ne "fMet")
+					{
+						$tRNA->sort_multi_models("model");
+						my ($met_iso_model, $met_iso_score, $met_iso_ss) = $tRNA->get_model_hit("cyto", $tRNA->isotype());
+						my ($ile2_iso_model, $ile2_iso_score, $ile2_iso_ss) = $tRNA->get_model_hit("cyto", "Ile2");
+						if ($ile2_iso_score > 0 and $met_iso_score > 0)
+						{
+							if (($score - $ile2_iso_score) <= 5 and ($ile2_iso_score - $met_iso_score) >= 5 and $tRNA->score() > 50)
+							{
+								$tRNA->isotype("Ile2");
+								$tRNA->tRNAscan_id($tRNA->seqname().".tRNA".$tRNA->id()."-".$tRNA->isotype().$tRNA->anticodon());
+							}
+						}
+					}
 				}				
 			}			
 		

tRNAscan-SE.src

-#! /usr/bin/perl
+#! @PERL@
 #
 # --------------------------------------------------------------------
 # tRNAscan-SE: a program for improved detection of transfer RNA
 #              genes in genomic sequence
 #
-# Version 2.0
+# Version 2.0.3
 #
-# Copyright (C) 2017 Patricia Chan and Todd Lowe 
+# Copyright (C) 2019 Patricia Chan and Todd Lowe 
 #
 # School of Engineering, University of California, Santa Cruz
 # lowe@soe.ucsc.edu
@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;
 use tRNAscanSE::MultiResultFile;
 use tRNAscanSE::SS;
 
-our $version = "2.0"; 
-our $release_date = "December 2017";
+our $version = "2.0.3"; 
+our $release_date = "April 2019";
 our $program_id = "tRNAscan-SE-".$version;
 
 # modified by 'make'
@@ -126,7 +126,7 @@ if (($stats->numscanned() == 0) && ($opts->eufind_mode() || $opts->tscan_mode()
     }
     else
     {
-        die "\nFATAL: No sequences in FASTA format found in file ".$opts->fastafile()."\n\n";
+        die "\nFATAL: No sequences in FASTA format found in file ".$opts->fasta_file()."\n\n";
     }
 }
 
@@ -621,7 +621,7 @@ sub error_handler
 
 sub display_credits
 {
-    print STDERR "Copyright (C) 2017 Patricia Chan and Todd Lowe\n",
+    print STDERR "Copyright (C) 2019 Patricia Chan and Todd Lowe\n",
                  "                   University of California Santa Cruz\n",
                  "Freely distributed under the GNU General Public License (GPLv3)\n\n";
 }
@@ -1881,9 +1881,9 @@ sub set_options
     
     if ($opt_thread != 999)
     {
-		if ($opt_thread < 1)
+		if ($opt_thread < 0)
         {
-            die "FATAL: Number of threads for running Infernal must be at least 1.\n";
+            die "FATAL: Number of threads for running Infernal must be at least 0.\n";
 		}
         if ($opt_eufind || $opt_tscan || $opt_cove || $opt_legacy)
         {