Question

我有一个.ini文件，其中一个选项是： [LDdecay] ;确定是否检查SN衰变的LD衰减 ;＆＃34; 0＆＃34;是假的（不），＆＃34; 1＆＃34;仅适用于GBS，＆＃34; 2＆＃34;仅适用于SoySNP50K，＆＃34; 3＆＃34;仅适用于合并，＆＃34; 4＆＃34;适用于所有人（GBS，SoySNP50K和Merge）衰变= 1

对于第69,72,80,88和96行（基本上是if或elif语句的任何地方），我不断收到以下错误： [::期望整数表达式

我清楚地忽略了一些事情，因为我曾与elif和其他人成功合作，所以任何能够抓住故障的人都会受到很大的影响。感谢

#!/bin/bash


#################################################
#                                               #
#    A base directory must be created and       #
#    the config file must be placed in there    #
#                                               #
#################################################



#check if config file was supplied
if [ $# -ne 1 ]; then #if number of argument is different than 1
  echo -e "Usage: run_pipeline_cfg.sh <configuration file>" #print     error message
  exit 1 #stop script execution
fi

#Parse the info from the ini file
ini=$(readlink -m "$1")
source <(grep="$ini" | \
sed -e "s/[[:space:]]*\=[[:space:]]*/=/g" \
-e "s/;.*$//" \
-e "s/[[:space:]]*$//" \
-e "s/^[[:space:]]*//" \
-e "s/^\(.*\)=\([^\"']*\)$/\1=\"\2\"/")




#ini="/home/directory/Initiator.ini" #debug

#Retrieve the base directory path
baseDir=$(dirname "$ini")


#Create required directory structure
logs="$baseDir/logs"
LDdecay="$baseDir/LDdecay"
imputed="$baseDir/imputed"


#dont create if already exists
[[ -d "$logs" ]] || mkdir "$logs"
[[ -d "$LDdecay" ]] || mkdir "$LDdecay"
[[ -d "$imputed" ]] || mkdir "$imputed"




#find imputed vcf files
if [ -e $imputed ] ; then
  echo -e "Folder with imputed vcf files exists. Determining if calculating LD decay"
else
  echo -e "Folder with imputed vcf files does not exist. Cannot calculate LD decay."
  exit 1
fi


#######################################################
#                                                     #
#      Create LD decay files for LD decay plots       #
#                                                     #
#######################################################

#determine on which files to perform LD decay calculations
#"0" is false (no), "1" is true for GBS only, "2" is true for Microarray only, "3" is true for Integrated only, "4" is true for all (GBS, Microarray and Integrated)

if [ "$decay" -eq 0 ]; then
  printf "LD decay rates not calculated" | tee -a $logs/log.txt;

elif [ "$decay" -eq 1 ]; then
  #perform LD decay calculation for GBS only
  zcat $imputed/GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
  plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
  rm $LDdecay/GBS_MAF0.01.vcf

  printf "LD decay for GBS dataset completed" | tee -a $logs/log.txt

elif [ "$decay" -eq 2 ]; then
    #perform LD decay calculation for microarray only
  zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
  plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
  rm $LDdecay/microarray_MAF0.01.vcf

  printf "LD decay for microarray dataset completed" | tee -a $logs/log.txt

elif [ "$decay" -eq 3 ]; then
  #perform LD decay for Merged dataset only
  zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
  plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
  rm $LDdecay/Integrated_MAF0.01.vcf

  printf "LD decay calculation for Integrated dataset complete" | tee -a $logs/log.txt

elif [ "$decay" -eq 4 ]; then
  #perform LD decay for Merged, GBS and SoySNP50K datasets
  zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
  plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
  rm $LDdecay/Integrated_MAF0.01.vcf

  zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
  plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
  rm $LDdecay/microarray_MAF0.01.vcf

  zcat $imputed/snp_imputed_GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
  plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
  rm $LDdecay/GBS_MAF0.01.vcf

  printf "LD decay calculation completed for Integrated, GBS and SoySNP50K datasets completed" | tee -a $logs/log.txt

else
  echo "Wrong LD Decay calculation setup"
  exit 1
fi

Answer 1

考虑将elsif链更改为case语句。它应该试图使测试具有整数参数，并且它更清晰，更容易扩展：

case $decay in
  0)
    printf "LD decay rates not calculated" | tee -a $logs/log.txt;
    ;;

  1)
    #perform LD decay calculation for GBS only
    zcat $imputed/GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
    plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
    rm $LDdecay/GBS_MAF0.01.vcf

    printf "LD decay for GBS dataset completed" | tee -a $logs/log.txt
    ;;

  2)
    #perform LD decay calculation for microarray only
    zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
    plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
    rm $LDdecay/microarray_MAF0.01.vcf

    printf "LD decay for microarray dataset completed" | tee -a $logs/log.txt
    ;;

  3)
    #perform LD decay for Merged dataset only
    zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
    plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
    rm $LDdecay/Integrated_MAF0.01.vcf

    printf "LD decay calculation for Integrated dataset complete" | tee -a $logs/log.txt
    ;;

  4)
    #perform LD decay for Merged, GBS and SoySNP50K datasets
    zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
    plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
    rm $LDdecay/Integrated_MAF0.01.vcf

    zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
    plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
    rm $LDdecay/microarray_MAF0.01.vcf

    zcat $imputed/snp_imputed_GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
    plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
    rm $LDdecay/GBS_MAF0.01.vcf

    printf "LD decay calculation completed for Integrated, GBS and SoySNP50K datasets completed" | tee -a $logs/log.txt
    ;;

  *)
    echo "Wrong LD Decay calculation setup"
    exit 1
    ;;
esac

如果elif else有多个选项错误

1 个答案: