脚本记录之snp-calling【终】

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最新推荐文章于 2024-05-20 16:40:58 发布

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分类专栏：学习记录文章标签： linux shell

本文链接：https://blog.csdn.net/mushroom234/article/details/111305018

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CSDN：记录bug史

#!/bin/bash
#PBS -N kissplice
#PBS -l nodes=zhangxclab002:ppn=12
#PBS -q batch
#PBS -V
#PBS -S /bin/bash
myPATH="/home/usr/transnp"
rawdata="/home/usr/transnp/rawdata"

#Write before all:
#		if you use conda, please activate your environment needed in these scripts;
#		1. and 2. step can run together without conflict
#1. transdecoder1.sh & transdecoder2.sh : output .bed files;
#2. kissplice.sh : output *type_0a.fa file;
#3. blat.sh needs rawdata,type_0a.fa,blat.psl;
#4. kiss2reftran.sh relies on the previous four script-outputs;
#5. finally run clean.sh to put the same file type to one directory, thus clean the screen to make tidy results.

transdecoder1.sh(){
   
##############################################################transdecoder1.sh################################################
#判断.fa文件并按顺序执行
cd $myPATH
dir=$(ls -l $rawdata |awk '!/^d/ {print $NF}' |grep -i ".fa" )
for i in $dir
	do
		/home/usr/packages/TransDecoder-master/TransDecoder.LongOrfs -t $rawdata/$i 
	done
}

transdecoder2.sh(){
   
##############################################################transdecoder2.sh################################################
#判断.fa文件并按顺序执行
cd $myPATH
dir=$(ls