Question

在下面的bash中，用户选择要在第一个select中使用的文件，然后该文件中的该数字用于自动“选择the second file. The problem is that when the second file is selected the path appears in the name so the bash”错误。我似乎无法解决这个问题，需要一些帮助。我为长篇文章道歉，只是试图确保所需的所有文件都在这里。谢谢你:)。

Bash

FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools
ANNOVARDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar

PS3="please select a file to analyze with a panel: " # specify file
select file in $(cd ${FILESDIR};ls);do break;done
    file1=`basename ${FILESDIR}/${file}`
    printf "File 1 is: ${file1} and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel"
for file in /home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools/$file; do
 bname=$(basename $file)
 pref=${bname%%.txt}
 grep -wFf /home/cmccabe/Desktop/NGS/panels/EPILEPSY_unix_trim.bed $file > /home/cmccabe/Desktop/NGS/API/5-14-2016/panel/reads/${pref}_EPILEPSY.txt
 done
# filter vcf
printf "\n\n"
file2=`basename $(ls ${ANNOVARDIR}/${file%%_*}*)`
        printf "File 2 is: ${file2} and will be used filtered using the epilepsy genes"
 pref=${bname%%}
 awk 'NR==FNR{for (i=1;i<=NF;i++) a[$i];next} FNR==1 || ($7 in a)' /home/cmccabe/Desktop/NGS/panels/EPILEPSY_unix_trim.bed $file2 | awk '{split($2,a,"-"); print a[1] "\t" $0}' | cut -f2-> /home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/panel/annovar/${pref}_Epilepsyfiltered.bed

如果用户选择12311_base_counts.txt，

首先选择的文件`

12311_base_counts.txt
45611_base_counts.txt

第二次选择的文件

12311_variant_strandbias_readcount.vcf.hg19_multianno_removed_final (this one is automatically selected because it has the same starting digits as the original file)
45611_variant_strandbias_readcount.vcf.hg19_multianno_removed_final

bash with error （this portion of the path is the problem I think, /home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools/）

1) 12311_base_counts.txt   
2) 45611_base_counts.txt   

please select a file to analyze with a panel: 7
File 1 is: T31129_base_counts.txt and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for visualization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel

ls: cannot access /home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar//home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools/T31129*: No such file or directory/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools/
File 2 is:  and will be used filtered using the epilepsy genes

Answer 1

应该是：

file2=$(ls ${ANNOVARDIR}/`basename ${file%%_*}`*)

bash删除第二个选择中的路径

1 个答案: