用匹配将目录中的特定文件扩展名重命名为bash中的另一个文件

Question

我在目录.bam中有一套特定的下载文件集(全部以/home/cmccabe/Desktop/NGS/API/2-15-2016结尾)。我要做的是使用与$2在name中的匹配来重命名下载的文件。为了使事情更复杂，文件夹的日期是唯一的，在name的标题中，匹配日期是存在的，也是name中匹配的位置。我不知道该如何做，也不知道是否可能。谢谢:)。

文件夹/home/cmccabe/Desktop/NGS/API/2-15-2016的内容

IonXpress_001.bam
IonXpress_002.bam
IonXpress_003.bam
IonXpress_007.bam
file1.gz
file2.gz

名称

2-15-2016
IonXpress_001.bam testname1_12345
IonXpress_002.bam testname2_45678
IonXpress_003.bam testname3_9012
IonXpress_007.bam testname1_12345-
2-19-2016
IonXpress_001.bam testname5_00000
IonXpress_002.bam testname6_11111
IonXpress_003.bam testname7_1213
IonXpress_007.bam testname8_78524

期望结果

testname1_12345.bam
testname2_45678.bam
testname3_9012.bam
testname1_12345.bam
file1.gz
file2.gz

bash到目前为止

logfile=/home/cmccabe/Desktop/NGS/API/2-15-2016/process.log
for f in /home/cmccabe/Desktop/NGS/API/2-15-2016/*.bam ; do
echo "patient identifier creation: $(date) - File: $f"
bname=$(basename $f)
pref=${bname%%.bam}
while read from to ; do
for i in $f* ; do
if [ "$i" != "${i/$from/$to}" ] ; then
  mv $i ${i/$from/$to}
fi
done < names.txt
echo "End patient identifier creation: $(date) - File: $f"
done >> "$logfile"

编辑：

for f in /home/cmccabe/Desktop/NGS/API/2-12-2016/*.bam ; do
  bname=$(basename $f)
  cmd=$(sed -n "/$f/,/[0-9]{1,2}-[0-9]{1,2}-20[0-9]{2}/{s/\(.*\.bam\) \(.*\)/mv \1 \2/p}" /home/cmccabe/Desktop/NGS/panels/names.txt)
  echo "$cmd"
done
sed: -e expression #1, char 4: extra characters after command

Answer 1

您可以将此for循环与awk一起使用。

cd /home/cmccabe/Desktop/NGS/

for file in API/*/*.bam; do
   f="${file##*/}"
   path="${file%/*}"
   dt="${path##*/}"
   mv "$file" "$path/$(awk -v dt="$dt" -v f="$f" 'NF==1 {
               p=$0==dt ? 1 : 0; next} p && $1==f{print $2}' names.txt)"
done

Answer 2

您可以这样做，我在sed中使用了f变量：

 cmd=$(sed -n "/$f/,/[0-9]{1,2}-[0-9]{1,2}-20[0-9]{2}/{s/\(.*\.bam\) \(.*\)/mv \1 \2/p}" names.txt)
 # for testing use echo and this will also save what you just tried 
 #to do to your log file :) just in case.
 echo "$cmd"
 # when it works the way you want
 # uncomment the next line and it will execute your command :)
 #eval "$cmd"

这是告诉sed不要打印用-n读取的行。

然后是从匹配日期($f)到下一个数据模式的行( DD-DD-20DD (regex: 0-9{1,2}-0-9{1,2}-200-9{2}) )在{}之间执行命令。

{}中的命令是一个替换的"s“命令，它将匹配一个模式并替换为另一个模式。

我告诉它将字符串一路带到.bam，并将它放在(和)之间，然后匹配行的其余部分，并将其放到另一个组中。

替换模式是mv字符串，后面是在匹配模式中捕获的组1，然后是组2中的字符串，有效地创建了mv file.bam new_filename命令的列表。

然后将它们存储在cmd变量中。

eval将执行命令..。

我以您的name.txt文件的示例内容为例，并进行了转换以说明：

 ~$echo "2-12-2016
 IonXpress_001.bam testname1_12345
 IonXpress_002.bam testname2_45678
 IonXpress_003.bam testname3_9012
 IonXpress_007.bam testname1_12345-
 2-19-2016
 IonXpress_001.bam testname5_00000
 IonXpress_002.bam testname6_11111
 IonXpress_003.bam testname7_1213
 IonXpress_007.bam testname8_78524" |sed -n "/$f/,/[0-9]{1,2}-[0-9]{1,2}-20[0-9]{2}/{s/\(.*\.bam\) \(.*\)/mv \1 \2/p}"
 mv IonXpress_001.bam testname1_12345
 mv IonXpress_002.bam testname2_45678
 mv IonXpress_003.bam testname3_9012
 mv IonXpress_007.bam testname1_12345-
 mv IonXpress_001.bam testname5_00000
 mv IonXpress_002.bam testname6_11111
 mv IonXpress_003.bam testname7_1213
 mv IonXpress_007.bam testname8_78524

UPDATE:从您的评论和编辑中我看到我不是很擅长解释:)我这里是您脚本的编辑版本。我将假设您在运行此文件时位于/home/cmccabe/Desktop/NGS/API/文件夹中。如果没有，我相信你会知道如何作出改变或进行辩论。

 logfile=/home/cmccabe/Desktop/NGS/API/2-15-2016/process.log
 # no need to loop for each file ending in bam as the name file
 # will be our driver. After all if the entry is not present in
 # the name file then we really cannot do anything.

 # First lets get the date from the folder name:
 #    pwd will return the current working directory (which we are supposed 
 #        to be in the directory to process)
 #    basename will strip all but the last folder name, hence the date
 date_to_process=$(basename $(pwd))

 # variable to store name file path (hint change this to where it really is or pass as argument to script)
 name_file_path = "/home/cmccabe/Desktop/NGS/panels/names.txt"

 # from the name file build the file move (mv) commmands using sed 
 # as described before and store that command in the cmd variable.
 # note that I added a couple of echo commands to have the same output you 
 # were trying to do. I also split the command on multiple lines 
 # for clarity (well I hope it makes it more clear at least).
 cmd=$(sed -n "/$date_to_process/,/[0-9]{1,2}-[0-9]{1,2}-20[0-9]{2}/{
    s/\(.*\.bam\) \(.*\)/echo \"Start patient identifier creation: \$(date) - File: \1\"\n mv \1 \2\n echo \"End patient identifier creation: \$(date) - File: \1\"/p
 }" $name_file_path)

 # print the generated commands to you can see what it did.
 echo "about to execute this command: 
 $cmd" 

 # execute the commands to perform the move operations and send the 
 #output to the log file. Make sure to pipe stderr (errors) to the log file 
 # too so you will know what/if something failed. (using 2>&1) this will make all stderr go to the same pipe as stdin. 
 eval "$cmd" >> "$logfile" 2>&1