diff --git a/LTR_retriever b/LTR_retriever index 67eb200..d828d51 100755 --- a/LTR_retriever +++ b/LTR_retriever @@ -5,11 +5,11 @@ 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="v2.9.8"; +my $version="v2.9.9"; my $help=" -############################## +############################ ### LTR_retriever $version ### -############################## +############################ A program for accurate identification of LTR-RTs from outputs of LTRharvest and LTR_FINDER, generates non-redundant LTR-RT library for genome annotations. @@ -199,9 +199,9 @@ die "\nERROR: The specified file $inmgescan does not exist.\n\n" if $inmgescan!~ die "\nERROR: The specified file $inharvest does not exist.\n\n" if $inharvest!~/^$/ and !-e "$inharvest"; print " -########################## +############################ ### LTR_retriever $version ### -##########################\n +############################\n Contributors: Shujun Ou, Ning Jiang\n For LTR_retriever, please cite: @@ -304,7 +304,7 @@ $PlantP="$PlantP_base.$rand"; chomp ($date=`date +"%m-%d-%y_%H%M"`); if ($step eq "Init" and `ls $genome*|wc -l`>15){ print "\n\t\t\t\tPrevious LTR_retriever results found, backed up to LTRretriever-pre$date\n\n"; - `mkdir LTRretriever-pre$date; mv $genome*.out $genome*.out.gff* $genome*.LAI $genome*.LTRlib* $genome*defalse $genome*.ltrTE* $genome*.retriever.* $genome*.prelib* $genome*.pass.list* $genome*.out*size.list $genome.out.LTR.distribution.txt LTRretriever-pre$date/ 2>/dev/null`; + `mkdir LTRretriever-pre$date; mv $genome*.tbl $genome*.out $genome*.cat* $genome*.masked $genome*.out.gff* $genome*.LAI $genome*.LTRlib* $genome*defalse $genome*.ltrTE* $genome*.retriever.* $genome*.prelib* $genome*.pass.list* $genome*.out*size.list $genome.out.LTR.distribution.txt LTRretriever-pre$date/ 2>/dev/null`; } ## check if genome writable