Looping through files defined by `*` in a variable in BASH

Question

I want to be able to specify a directory with fastq files with a script that will loop through all the files and do some stuff. Here is my attempt:

threads=24
current_path=`pwd`
input_file=${current_path}/raw/

files=${current_path}/raw/*

for file in ${files}; do 

    output_file=${current_path}/${file}_out/
    mkdir -m gu=wrx,o=rx ${output_file}

    spades.py \
    --s1 ${input_file}${file} \
    -t ${threads} \
    --plasmid \
    --careful \
    -o ${output_file}

done

So in this script I get an error: cannot make directory, directory does not exist The script generates a /home folder. I don't know if I am specifying the files incorrectly or if I am using the for loop incorrectly.

Thank you!

For isolating the error, first write the for loop echoing the file name with v.gr. `echo about to process: "$file"`. If the current path contains spaces, you will probably identify an error because the file name will be split on two iterations of the loop. — Pierre François, Nov 20 '19 at 11:52
See https://stackoverflow.com/questions/301039/how-can-i-escape-white-space-in-a-bash-loop-list for looping over files with white space in the path. — Pierre François, Nov 20 '19 at 11:57
@oguzismail nope it is exactly like this `/home/user/lustre/article_5` — Roelof Coertze, Nov 20 '19 at 12:15
@roelofco : So maybe some entries in the `raw` directory have spaces? — user1934428, Nov 20 '19 at 12:21
@roelofco : _I get an error_ is a somewhat poor description of an error. Did you ever consider, that people will need to know, what kind of error you get? — user1934428, Nov 20 '19 at 12:23
It would be interesting to know the output of `pwd`. If it is `/home`, a common user is not allowed to create a directory there. — Pierre François, Nov 20 '19 at 13:15
Look at the result of `echo "$output_file => mkdir -m gu=wrx,o=rx ${output_file}"` — Walter A, Nov 20 '19 at 14:47

score 0 · Answer 1 · answered Nov 20 '19 at 17:02

0

you concatenate full path to file with folder in line

output_file=${current_path}/${file}_out/

it should be

output_file=${file}_out/

answered Nov 20 '19 at 17:02

Maxim Sagaydachny

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Looping through files defined by `*` in a variable in BASH

1 Answers1