[med-svn] [Git][med-team/trnascan-se][master] 5 commits: routine-update: New upstream version
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jul 13 14:42:48 BST 2023
Andreas Tille pushed to branch master at Debian Med / trnascan-se
Commits:
0d58c404 by Andreas Tille at 2023-07-13T15:38:12+02:00
routine-update: New upstream version
- - - - -
ad5dd544 by Andreas Tille at 2023-07-13T15:38:13+02:00
New upstream version 2.0.12+ds
- - - - -
1091cbd0 by Andreas Tille at 2023-07-13T15:38:45+02:00
Update upstream source from tag 'upstream/2.0.12+ds'
Update to upstream version '2.0.12+ds'
with Debian dir e324796ee76cc407bf0e7bbaa521e8969a95faf8
- - - - -
fac12926 by Andreas Tille at 2023-07-13T15:38:45+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
0789e2fb by Andreas Tille at 2023-07-13T15:40:35+02:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- MitoHighConfidenceFilter.in
- debian/changelog
- debian/control
- lib/tRNAscanSE/CM.pm
- lib/tRNAscanSE/Utils.pm
- tRNAscan-SE.src
Changes:
=====================================
MitoHighConfidenceFilter.in
=====================================
@@ -588,6 +588,7 @@ sub write_ss_file
my $print_line = "";
my $include = 0;
my $tag = "";
+ my $has_note = 0;
my $ct = 0;
print "Status: Writing secondary structure file $file_names{output_tRNAscan_ss}\n";
@@ -603,6 +604,7 @@ sub write_ss_file
$print_line = $line;
$include = 0;
$tag = "";
+ $has_note = 0;
$ct++;
print STDERR "." if ($ct % 1000 == 0);
@@ -656,9 +658,14 @@ sub write_ss_file
{
$print_line .= $line;
}
+ $has_note = 1;
}
elsif (index($line, " * | * | * |") > -1)
{
+ if ($tag ne "" and $has_note == 0)
+ {
+ $print_line .= "\n";
+ }
$print_line .= $line;
}
elsif ($line =~ /^Seq:\s\S+$/)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+trnascan-se (2.0.12+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 13 Jul 2023 15:39:15 +0200
+
trnascan-se (2.0.10+ds-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
autoconf-archive,
infernal
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
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
=====================================
lib/tRNAscanSE/CM.pm
=====================================
@@ -1095,7 +1095,7 @@ sub decode_nci_tRNA_properties
}
}
$mat_seq .= substr($precursor_seq, $introns[scalar(@introns)-1]->{rel_end});
-
+
if (uc($mat_seq) eq uc($trna->mat_seq()))
{
$trna->seq($trna->mat_seq());
@@ -1659,14 +1659,13 @@ sub scan_noncanonical_introns
if ($ret_value)
{
$padded_seq = $clip_seq;
- $previous_intron_len = $intron_len;
+ $previous_intron_len += $intron_len;
$rnd2 = 1;
if ($duplicate)
{
$add_ci = 1;
}
}
-
$arrayCMscanResults->get_next_cmsearch_hit($cm_intron);
}
}
@@ -1697,7 +1696,7 @@ sub scan_noncanonical_introns
if ($ret_value)
{
$padded_seq = $clip_seq;
- $previous_intron_len = $intron_len;
+ $previous_intron_len += $intron_len;
if ($duplicate)
{
$add_ci = 1;
@@ -1891,7 +1890,7 @@ sub check_intron_validity
my $log = $global_vars->{log_file};
my $ret_value = 1;
my $duplicate = 0;
-
+
my ($pre_intron, $intron, $post_intron, $pre_intron_seq, $intron_seq, $post_intron_seq);
if ($cm_intron->ss() =~ /^([\<\-\.]{11,})(\-\<[<.]+[_.]{4,}[>.]{9,}\-[.]*\-)([-.>]+)$/)
{
@@ -1908,7 +1907,6 @@ sub check_intron_validity
$intron_seq =~ s/-//g;
$pre_intron_seq =~ s/-//g;
$post_intron_seq =~ s/-//g;
-
$log->debug("Found intron ".$intron_seq." for ".$tRNA->tRNAscan_id());
}
else
=====================================
lib/tRNAscanSE/Utils.pm
=====================================
@@ -19,7 +19,7 @@ our %comp_map = ( # Complement map
'A' => 'T', 'T' => 'A', 'U' => 'A',
'G' => 'C', 'C' => 'G',
'Y' => 'R', 'R' => 'Y',
- 'S' => 'W', 'W' => 'S',
+ 'S' => 'S', 'W' => 'W',
'M' => 'K', 'K' => 'M',
'B' => 'V', 'V' => 'B',
'H' => 'D', 'D' => 'H',
=====================================
tRNAscan-SE.src
=====================================
@@ -4,7 +4,7 @@
# tRNAscan-SE: a program for improved detection of transfer RNA
# genes in genomic sequence
#
-# Version 2.0.10
+# Version 2.0.12
#
# Copyright (C) 2022 Patricia Chan and Todd Lowe
#
@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;
use tRNAscanSE::MultiResultFile;
use tRNAscanSE::SS;
-our $version = "2.0.10";
-our $release_date = "Sept 2022";
+our $version = "2.0.12";
+our $release_date = "Nov 2022";
our $program_id = "tRNAscan-SE-".$version;
# modified by 'make'
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/-/compare/64d4e321fec0ff6e5c930d3b3cab0f1b4e1116e4...0789e2fba79e25a9a7625dcc493e1a13a35b502c
--
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/-/compare/64d4e321fec0ff6e5c930d3b3cab0f1b4e1116e4...0789e2fba79e25a9a7625dcc493e1a13a35b502c
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