From 84ca5fcd1ab4489f528d288bda13804b20fe17f4 Mon Sep 17 00:00:00 2001
From: oushujun <shujun.ou.1@gmail.com>
Date: Tue, 11 Jul 2023 01:25:20 -0400
Subject: [PATCH] fix bug #153

---
 LTR_retriever | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/LTR_retriever b/LTR_retriever
index f4cc65c..aa98963 100755
--- a/LTR_retriever
+++ b/LTR_retriever
@@ -5,7 +5,7 @@ use File::Basename;
 
 ##Supported dependent program versions (or up): GenomeTools/1.5.1, BLAST+/2.2.25, BLAST/2.2.25, HMMER/3.1b1, RepeatMasker/3.3.0, CDHIT/4.5.6, Tandem Repeats Finder 4.07b, and Perl 5.0.0
 
-my $version="v2.9.4";
+my $version="v2.9.5";
 my $help="
 ############################
 ### LTR_retriever $version ###
@@ -265,7 +265,7 @@ die "Error: RepeatMasker is not found in the RepeatMasker path $repeatmasker!\n"
 `cp $script_path/database/dummy060817.fa ./dummy060817.fa.$rand`;
 `${blastplus}makeblastdb -in ./dummy060817.fa.$rand -dbtype nucl`;
 my $RM_test=`${repeatmasker}RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa.$rand -lib dummy060817.fa.$rand 2>/dev/null`;
-die "Error: The RMblast engine is not installed in RepeatMasker!\n" unless $RM_test=~s/done//gi;
+die "Error: The RMblast engine is not installed in RepeatMasker!\n" unless $RM_test=~s/(done|No repetitive sequences were detected)//gi;
 `rm dummy060817.fa.$rand* 2>/dev/null`;
 
 #cd-hit-est
@@ -722,7 +722,7 @@ my $index=$_[0];
 `touch $index.retriever.scn.extend.fa.aa.tbl` unless -s "$index.retriever.scn.extend.fa.aa.tbl";
 `perl $script_path/bin/annotate_TE.pl $index.retriever.scn.extend.fa.aa.tbl > $index.retriever.scn.extend.fa.aa.anno`;
 `$TEsorter $index.retriever.scn.extend.fa --disable-pass2 -p $threads 2>/dev/null`;
-`awk '{print \$1"\\t"\$2"\\t"\$3"\\t"\$6"\\t"\$7}' $index.retriever.scn.extend.fa.rexdb.cls.tsv >> $index.retriever.scn.extend.fa.aa.anno`;
+`awk '{print \$1"\\t"\$2"\\t"\$3"\\t"\$6"\\t"\$7}' $index.retriever.scn.extend.fa.rexdb.cls.tsv | perl -nle 's/([0-9]+\\.\\.[0-9]+)_(.*:[0-9]+\\.\\.[0-9]+)/\$1\\|\$2/; print \$_' >> $index.retriever.scn.extend.fa.aa.anno`;
 
 # identify intact LTR retrotransposons
 `perl $script_path/bin/LTR.identifier.pl $index -list $index.retriever.scn -seq $index.retriever.scn.extend.fa -anno $index.retriever.scn.extend.fa.aa.anno -flanksim $flanksim -flankmiss $flankmiss -flankaln $flankaln -minlen $minlen $tsdaln -u $miu -threads $threads -blastplus $blastplus -motif @motif > $index.defalse`;