Script recording of snp-calling

Please move: snp-calling recorded by script [End]

#!/bin/bash
#PBS -N transdecoder
#PBS -l nodes=zhangxclab002:ppn=12
#PBS -q batch
#PBS -V
#PBS -S /bin/bash
#RS144A.fa  RS150A.fa  RS247A.fa  RS255A.fa
#sample

myPATH="/home/chenss/kissplices"
#判断.fa文件并按顺序执行
dir=$(ls -l $myPATH |awk '!/^d/ {print $NF}' |grep -i ".fa" )
for i in $dir
do
	comma= " -r $i "
	comman= $comman + $comma
	echo "running $i"
	/home/chenss/packages/TransDecoder-master/TransDecoder.LongOrfs -t $i &
	wait
	/home/chenss/packages/TransDecoder-master/TransDecoder.Predict -t $i &
done
echo "TransDecoder over"

#kissplice snp calling
#判断.fa文件并按顺序执行
myPATH="/home/chenss/kissplices"
dir=$(ls -l $myPATH |awk '!/^d/ {print $NF}' |grep -i ".fa" )
for i in $dir
do
	comma= " -r $i "
	comman= $comman + $comma
done
echo "start snp-calling"
eval "kissplice $comman -s 1 " &
wait
echo "kissplice over"


#判断kissplice是否生成所需文件
myPATH="/home/chenss/kissplices"
files=$(ls $myPATH/results/*type_0a.fa 2> /dev/null | wc -l)
if [ "$files" != "0" ] ;then  #如果存在文件
	echo "start BLAT"
	dir=$(ls -l $myPATH |awk '!/^d/ {print $NF}' |grep -i ".fa" )
	for i in $dir
		do
		/home/chenss/packages/blatsuite/blat -minIdentity=80 -q=rna $myPATH/$i $myPATH/results/*type_0a.fa output_$i.psl &
		done
	wait 
	echo "BLAT all over!"
else
	echo "type_0a.fa not exist, please check kissplice output"
fi

Editor's note: It's tiring to write the script. I wrote it all morning.
December 16, 2020: This script hasn't been changed. Some syntax and python perl strings are missing, so it can't run anyway. It feels like this:
"I had a breakfast today, おいしい, it feels very nice." I
don't want to delete it, but leave a memory.