retriever_flow

#!/bin/bash
#********************************************************************
#Author: Beirui Niu
#Group: Lu Lab
#Date： 2021-10-29
#FileName： retriever.sh
#URL： 
#Description：这是聪明的钮蓓蕊写的第二个shell文件，主要是参照blast.sh做了一些修改，用来批量进行ltr_retriever，预计用时会很长。第一个误删了，不过没关系，反正以后还会写。
#********************************************************************
PATH=/data1/home/beirui/anaconda3/bin:/data1/home/beirui/anaconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/data1/home/beirui/.local/bin:/data1/home/beirui/bin
export PATH

#Storage
contigs_dir=/data1/home/beirui/data/unzip.contigs
workspace=/data1/home/beirui/workspace/02_retriever
software=/data1/home/beirui/software
contigs_file=(`ls $contigs_dir`)

for(( i=0;i<${#contigs_file[@]};i++))
do
contigs_name[i]=`echo ${contigs_file[i]} | cut -d . -f1`
done

echo ${contigs_file[@]}
echo ${contigs_name[@]}

#Function
function har_gt {
ln -s $contigs_dir/${contigs_file[i]}
$software/05_LTRharvest/bin/gt suffixerator -db ${contigs_file[i]} -indexname ${contigs_name[i]} -tis -suf -lcp -des -ssp -sds -dna
}
function har {
$software/05_LTRharvest/bin/gt ltrharvest -index ${contigs_name[i]} -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 -seqids yes > ${contigs_name[i]}.harvest.scn
}
function fin {
$software/04_LTR_FINDER_parallel/LTR_FINDER_parallel -seq ${contigs_file[i]} -threads 10 -harvest_out -size 1000000 -time 300
cat ${contigs_name[i]}.harvest.scn ${contigs_name[i]}.finder.combine.scn > ${contigs_name[i]}.rawLTR.scn
}
function ret {
$software/03_LTR_retriever/LTR_retriever -genome ${contigs_file[i]} -inharvest ${contigs_name[i]}.rawLTR.scn -threads 10 [options]
}
function lai {
$software/03_LTR_retriever/LAI -genome ${contigs_file[i]} -intact ${contigs_name[i]}.pass.list -all ${contigs_name[i]}.out [options]
}

#Calculate
echo "RETRIEVER:"
cd $workspace
for ((i=0; i<${#contigs_file[@]}; i++))
	do 
		joblist=($(jobs -p))
		while (( ${#joblist[*]} >= 20 ))
		do
			sleep 1
			joblist=($(jobs -p))
		done
		har_gt&
	done
wait
for ((i=0; i<${#contigs_file[@]}; i++))
	do 
		joblist=($(jobs -p))
		while (( ${#joblist[*]} >= 20 ))
		do
			sleep 1
			joblist=($(jobs -p))
		done
		har&
	done
wait
for ((i=0; i<${#contigs_file[@]}; i++))
	do 
		joblist=($(jobs -p))
		while (( ${#joblist[*]} >= 20 ))
		do
			sleep 1
			joblist=($(jobs -p))
		done
		fin&
	done
wait
for ((i=0; i<${#contigs_file[@]}; i++))
	do 
		joblist=($(jobs -p))
		while (( ${#joblist[*]} >= 20 ))
		do
			sleep 1
			joblist=($(jobs -p))
		done
		ret&
	done
wait
for ((i=0; i<${#contigs_file[@]}; i++))
	do 
		joblist=($(jobs -p))
		while (( ${#joblist[*]} >= 20 ))
		do
			sleep 1
			joblist=($(jobs -p))
		done
		lai&
	done

exit