在Bash中使用指定路径遍历目录

Question

pathToBins=$1

bins="${pathToBins}contigs.fa.metabat-bins-*"

for fileName in $bins
do
    echo $fileName

done

My goal is to attach a path to my file name. I can iterate over a folder and get the file name when I don't attach the path. My challenge is when I add the path echo fileName my regular expression no longer works and I get "/home/erikrasmussen/Desktop/Script/realLargeMetaBatBinscontigs.fa.metabat-bins-*" where the regular expression '*' is treated like a string. How can I get the path and also the full file name while iterating over a folder of files?

Answer 1

Although I don't really know how your files are arranged on your hard drive, a casual glance at "/home/erikrasmussen/Desktop/Script/realLargeMetaBatBinscontigs.fa.metabat-bins-*" suggests that it is missing a / before contigs . If that is the case, then you should change your definition of bins to:

bins="${pathToBins}/contigs.fa.metabat-bins-*"

However, it is much more robust to use bash arrays instead of relying on filenames to not include whitespace and metacharacters. So I would suggest:

bins=(${pathToBins}/contigs.fa.metabat-bins-*)
for fileName in "${bins[@]}"
do
    echo "$fileName"
done

Bash normally does not expand a pattern which doesn't match any file, so in that case you will see the original pattern. If you use the array formulation above, you could set the bash option nullglob , which will cause the unmatched pattern to vanish instead, leaving an empty array.