New upstream version 2.0.3 (4bb57dfe) · Commits · Debian Med / trnascan-se

EukHighConfidenceFilter.in

+24 −16

Original line number	Diff line number	Diff line
		@@ -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";

lib/tRNAscanSE/ArraytRNA.pm

+2 −12

Original line number	Diff line number	Diff line
		@@ -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

+28 −3

Original line number	Diff line number	Diff line
		@@ -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

+27 −0

Original line number	Diff line number	Diff line
		@@ -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

+9 −9

Original line number	Diff line number	Diff line
		#! /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)
		{