bash语句替换文本，解析json linux文本处理，解析json，替换txt里的字符串，正则表达式

bash语句替换文本，解析json

#!/bin/bash
# 这个脚本的目的是，
# 拿到输入的json文件；
# 解析json文件；
# 然后保证 Docker镜像顺利执行；

pwdPath=$0
echo "Hello! $pwdPath script is running..."
echo "###################################################################"
echo "This script is written by (If you have any problems. Please contact @@.com)"

jsonfilePath=$1 #用户输入的json路径
# 如果没有前端输入的json文件 则宣布退出
if [ ! "$1" ]; then
  echo "Usage: bash run_job.sh /Output/*.json|/Output/*.yaml /Input/[H5AD]"
  exit
else
  echo "input json filename is $jsonfilePath"
  species=`cat $jsonfilePath | jq -r '.species'`

  if test $species = "human"
  then
    indexDirPath="/ssd1//PBMC_human/star"
    gtfFilePath="/ssd1//PBMC_human/genes.gtf"
  elif test $species = "monkey"
  then
    indexDirPath="/ssd1//PBMC_monkey/star"
    gtfFilePath="/ssd1//PBMC_monkey/genes.gtf"
  elif test $species = "rat"
  then
    indexDirPath="/ssd1//PBMC_rat/star"
    gtfFilePath="/ssd1//PBMC_rat/genes.gtf"
  else
    echo "species error"
  fi

  fastq1FilePath=`cat $jsonfilePath | jq -r '.fastq1'`
  fastq2FilePath=`cat $jsonfilePath | jq -r '.fastq2'`
  CellNum=`cat $jsonfilePath | jq -r '.CellNum'`

  echo "index dir path is $indexDirPath"
  echo "gtf file path is $gtfFilePath"
  echo "fastq1 file path is $fastq1FilePath"
  echo "fastq2 file path is $fastq2FilePath"
  echo "CellNum is $CellNum"

  #接下来是修改runScSpark.sh 并执行
  runScSparkFilename="runScSpark.sh"

  indexOld=$(grep -oP '(?<=-genomeDir\s).*(?=\s\\)' $runScSparkFilename)
  sed -i "s|$indexOld|$indexDirPath|g" $runScSparkFilename

  gtfOld=$(grep -oP '(?<=-gtf\s).*(?=\s\\)' $runScSparkFilename)
  sed -i "s|$gtfOld|$gtfFilePath|g" $runScSparkFilename

  fq1Old=$(grep -oP '(?<=-fq1\s).*(?=\s\\)' $runScSparkFilename)
  sed -i "s|$fq1Old|$fastq1FilePath|g" $runScSparkFilename

  fq2Old=$(grep -oP '(?<=-fq2\s).*(?=\s\\)' $runScSparkFilename)
  sed -i "s|$fq2Old|$fastq2FilePath|g" $runScSparkFilename

  cellNumOld=$(grep -oP '(?<=-cellNumber\s).*(?=\s\\)' $runScSparkFilename)
  sed -i "s|$cellNumOld|$CellNum|g" $runScSparkFilename

  #bash runScSpark.sh

fi


echo "###################################################################"
echo "Finished!"