如果在另一个文件中找到搜索字符串，则可以删除目录中的文件。

Question

下面的bash几乎完成了。我唯一挣扎的部分是，在process.log中，如果找到字符串The bam file is corrupted and has been removed, please check log for reason.，则删除bash中相应的.bam ($f)。我补充说：

echo "The bam file is corrupted and has been removed, please check log for reason."
             [[ -f "$f" ]] && rm -f "$f"

在尝试这样做时，它看起来不管是移除最后一个.bam (在process.log NA19240.bam中(该文件中包含搜索字符串)，但它没有删除。相反，.bam (NS12911)中的最后一个process.log是(即使搜索字符串不在那里)。我无法解决这个问题，需要一些专家的帮助。我为这篇冗长的帖子道歉，只是想补充所有的细节。谢谢:)。

bash

logfile=/home/cmccabe/Desktop/NGS/API/5-4-2016/process.log
for f in /home/cmccabe/Desktop/NGS/API/5-4-2016/*.bam ; do
 echo "Start bam validation creation: $(date) - File: $f"
 bname=`basename $f`
 pref=${bname%%.bam}
 bam validate --in $f --verbose 2> /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/${pref}_validation.txt
 echo "End bam validation creation: $(date) - File: $f"
done >> "$logfile"
for file in /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/*.txt ; do
 echo "Start verifying $(date) - File: $file"
 bname=`basename $file`
 if $(grep -iq "(SUCCESS)" "${file}"); then
    echo "The verification of the bam file has completed sucessfully."
else
    echo "The bam file is corrupted and has been removed, please check log for reason."
             [[ -f "$f" ]] && rm -f "$f"
    echo "End of bam file verification: $(date) - File: ${file}"
fi
done >> "$logfile"

process.log

 Start bam validation creation: Fri May  6 13:20:48 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA12878.bam
 End bam validation creation: Fri May  6 13:24:15 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA12878.bam
 Start bam validation creation: Fri May  6 13:24:15 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA19240.bam
 End bam validation creation: Fri May  6 13:24:15 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA19240.bam
 Start bam validation creation: Fri May  6 13:24:15 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NS12911.bam
 End bam validation creation: Fri May  6 13:28:03 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NS12911.bam
 Start verifying Fri May  6 13:28:03 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NA12878_validation.txt
 The verification of the bam file has completed successfully.
 End of bam file verification: Fri May  6 13:28:03 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NA12878_validation.txt
 Start verifying Fri May  6 13:28:03 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NA19240_validation.txt
 The bam file is corrupted and has been removed, please check log for reason.
 End of bam file verification: Fri May  6 13:28:05 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NA19240_validation.txt
 Start verifying Fri May  6 13:28:05 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NS12911_validation.txt
 The verification of the bam file has completed successfully.
 End of bam file verification: Fri May  6 13:28:05 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NS12911_validation.txt

Answer 1

对我来说，完全复制你的环境有点困难，所以我不得不对你的设置和你的约束做一些假设。我认为这个过程可以通过许多方式简化或提高效率，但我主要关注的不是引入许多不必要的更改，而是将重点放在脚本的工作上。

尽管如此，我确实将处理重新安排到每个${pref}_validation.txt在创建后立即被验证的位置。

您是否可以尝试以下操作(注意:更新了脚本)。第一次，我跑得太快了，抄袭了错误的版本.)，并告诉我结果是什么：

#!/bin/bash

logfile="/home/cmccabe/Desktop/NGS/API/5-4-2016/process.log"

for f in /home/cmccabe/Desktop/NGS/API/5-4-2016/*.bam ; do
    echo "Start bam validation creation: $(date) - File: $f"
    bname="$(basename "$f")"
    pref="${bname%%.bam}"
    bam validate --in "$f" --verbose 2> "/home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/${pref}_validation.txt"
    echo "End bam validation creation: $(date) - File: $f"

    file="/home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/${pref}_validation.txt"

    echo "Start verifying $(date) - File: $file"

    if grep -iq "(SUCCESS)" "${file}"; then
        echo "The verification of the bam file has completed sucessfully."
    else
        if [[ -f "$f" ]]; then
            rm -f "$f"
            echo "The bam file is corrupted and has been removed, please check log for reason."
        fi
    fi

    echo "End of bam file verification: $(date) - File: ${file}"

done >> "$logfile"

希望结合在一个for循环中的两个步骤不会偏离您的某些流程需求。我发现这样做很有帮助，因为它允许一个更流线型的代码流，日志文件现在应该读起来如下：

Start bam validation creation: Fri May  6 13:20:48 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA12878.bam
End bam validation creation: Fri May  6 13:24:15 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA12878.bam
Start verifying Fri May  6 13:28:03 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NA12878_validation.txt
The verification of the bam file has completed successfully.
End of bam file verification: Fri May  6 13:28:03 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/NA12878_validation.txt
Start bam validation creation: Fri May  6 13:24:15 CDT 2016 - File: /home/cmccabe/Desktop/NGS/API/5-4-2016/NA19240.bam
...

高修改版本

我尝试了一个高度流线型和更具弹性的脚本版本。如果你也能查一下这个，我会感兴趣的：

#!/bin/bash

# basepath allows you to quickly move the script by updating this path
basepath="/home/cmccabe/Desktop/NGS/API/5-4-2016"

# give the logfile a name
logfile="${basepath}/process.log"

# for each .bam file in basepath do
for f in ${basepath}/*.bam ; do

    # validate the file with the bam command
    # capture the stdout, stderr and return code via some crazy bash fu
    eval "$({ cmd_err=$({ cmd_out=$( \
        bam validate --in "$f" --verbose \
      ); cmd_rtn=$?; } 2>&1; declare -p cmd_out cmd_rtn >&2); declare -p cmd_err; } 2>&1)"

    # check the return code for positive completion
    if [ "${cmd_ret}" -eq "0" ]; then
        printf -- "%s - bam validation completed for: %s\n" "$(date)" "${f}"

        # check for string "(SUCCESS)" in bam command standard output 
        if grep -iq "(SUCCESS)" <<< "${cmd_out}"; then
            printf -- "%s - Verification of the bam file has completed sucessfully.\n" "$(date)"
        else
            # verify the bam file exists and can be deleted
            if [[ -f "$f" ]] && rm -f "$f" ; then
                printf -- "%s - The bam file is corrupted and has been removed, please check log for reason.\n" "$(date)"
            else
                printf -- "%s - WARNING: The bam file is corrupted but the file could not be deleted.\n" "$(date)"
            fi
        fi
    else
        # The bam validate command above did not complete with a
        # satisfactory result. This should not really ever happen unless
        # the bam command does not exist or some serious error occurred
        # when executing the bam command.
        # Consider addition actions in addition to logging the outcome
        printf -- "%s - WARNING: bam validation failed for file: %s - [%s]\n" "$(date)" "${f}" "${cmd_err}"
    fi

done >> "$logfile"