I have a text file that contains a list of file paths. I want to loop through each line (file path), manipulate the file and store the manipulated file under a new name.

To do this I would like dynamically name the new file under file_$index so that each new file gets saved and not overwritten. Any ideas how to do this? my current code is:

for j in $(cat access.txt); do bcftools view $j -include 'maf[0]>0.0 & maf[0]<0.005' -output [FILE_NAME] ; done

i do not know how to dynamically change the file name i.e. to be file_$index. This would be equivalent of doing enumerate on a for loop in python. Note I cannot use the existing file path as that will overwrite the existing file which I do not want

In an ideal world i would manipulate the file path ($j) to extract part of the path as a new name. however I am not sure this is possible so file_$index also works.

CodePudding user response：

You can increment your own index with something like this:

i=$(( ${i:-0}   1 ))

then your output string can be

"$j_$i"

CodePudding user response：

A simple solution using while read

while read idx fpath; do echo "$(basename $fpath)_$idx.txt"; done <<<$(cat tmp.txt | nl)

Result

a_1.txt
b_2.txt
c_3.txt

For OP's code

bcftools view $j -include 'maf[0]>0.0 & maf[0]<0.005' -output "${fpath}_${idx}"

CodePudding user response：

Don't read lines with for

#!/usr/bin/env bash

index=1

while IFS= read -ru3 j; do
  bcftools view "$j" -include 'maf[0]>0.0 & maf[0]<0.005' -output "${j}_$index"
  ((index  ))
done 3< access.txt

In an ideal world i would manipulate the file path ($j) to extract part of the path as a new name.

As for the "$j" a Paramater Expansion can be use to manipulate/extract/replace whatever you want/wish with that variable.

• -ru3 is a shorthand for -r -u 3 It is using the FD 3 just in case bcftools is eating stdin , See help read

• ((index )) is an Arithmetic expression in bash.