[med-svn] [Git][med-team/trnascan-se][upstream] New upstream version 2.0.3
Steffen Möller
gitlab at salsa.debian.org
Sat Aug 3 14:37:47 BST 2019
Steffen Möller pushed to branch upstream at Debian Med / trnascan-se
Commits:
4bb57dfe by Steffen Moeller at 2019-08-03T13:22:55Z
New upstream version 2.0.3
- - - - -
5 changed files:
- EukHighConfidenceFilter.in
- lib/tRNAscanSE/ArraytRNA.pm
- lib/tRNAscanSE/CM.pm
- lib/tRNAscanSE/ScanResult.pm
- tRNAscan-SE.src
Changes:
=====================================
EukHighConfidenceFilter.in
=====================================
@@ -402,25 +402,33 @@ 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())
{
- my $alt_anticodon = $tRNA->anticodon();
- if (substr($tRNA->anticodon(), 0, 1) eq "A")
- {
- $alt_anticodon = "G".substr($tRNA->anticodon(), 1);
- }
- elsif (substr($tRNA->anticodon(), 0, 1) eq "G")
- {
- $alt_anticodon = "A".substr($tRNA->anticodon(), 1);
- }
-
- if (defined $aa_list{$tRNA->anticodon()} and defined $aa_list{$alt_anticodon} and defined $euk_aa_list{$alt_anticodon} and
- $ac_count->{$tRNA->anticodon()} > $ac_count->{$alt_anticodon})
- {}
- else
+ 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")
+ {
+ $alt_anticodon = "G".substr($tRNA->anticodon(), 1);
+ }
+ elsif (substr($tRNA->anticodon(), 0, 1) eq "G")
+ {
+ $alt_anticodon = "A".substr($tRNA->anticodon(), 1);
+ }
+
+ if (defined $aa_list{$tRNA->anticodon()} and defined $aa_list{$alt_anticodon} and defined $euk_aa_list{$alt_anticodon} and
+ $ac_count->{$tRNA->anticodon()} > $ac_count->{$alt_anticodon})
+ {}
+ else
+ {
+ $tag = "unexpected anticodon";
+ $tRNA_counts{ac_filter}++;
+ }
}
}
@@ -762,7 +770,7 @@ sub write_out_file
elsif (!$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}++;
$tag = "isotype mismatch";
=====================================
lib/tRNAscanSE/ArraytRNA.pm
=====================================
@@ -248,7 +248,7 @@ sub bsearch_id
{
if ($self->{ar_tRNAs}->[$i]->gtrnadb_id() lt $x)
{
- $l = $i+1;
+ $l = $i+1;
}
elsif ($self->{ar_tRNAs}->[$i]->gtrnadb_id() gt $x)
{
@@ -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
=====================================
@@ -1,12 +1,12 @@
-#! /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 at 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)
{
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/commit/4bb57dfe7327e8a81da79b902fb2c93fe48f571c
--
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/commit/4bb57dfe7327e8a81da79b902fb2c93fe48f571c
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