Infinite loop being generated using paste to stick together columns of tab delineated data

mbeavitt

10/23/23, 4:16 PM

Working with files containing many long columns of data, I'm trying to summarise all the data of one category as a series of tab delineated columns using paste. All of the files, of which there are 30, are named "output1234", and I want to cut out column six, and paste all the column sixes together in one file. I have a variable, $SAMPLE_ID which contains the "1234" part of each filename. Here is my BASH code:

#!/bin/bash

touch category6_table
for x in $SAMPLE_ID; do
   paste "$(cut -f6 output${x})" expression_table > expression_table

done

If I run this, it seems to get stuck in a loop and generate an infinitely long list of numbers.

EDIT: found a solution here https://unix.stackexchange.com/questions/141571/how-to-use-paste-command-for-many-files-whose-names-are-not-numbers-paste-colu

0 + 2

command-line

bash

paste

steeldriver

10/23/23, 5:15 PM

Because redirections are set up before commands are run, the `expression_table` file gets truncated (i.e. emptied) at each iteration - see this similar Q&A [add column and save file](https://askubuntu.com/questions/837968/add-column-and-save-file)

steeldriver

10/23/23, 5:16 PM

... I'd suggest trying something like `cut -f6 "output${x}" | paste expression_table - | sponge expression_table` where the `sponge` command is provided by the moreutils package

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