Iterating over directory with specified path in Bash

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?

rici rici · Accepted Answer · 2016-06-21T17:42:16

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.

Iterating over directory with specified path in Bash

1 Answers