CODEWITHSUNDEEP
linuxloops
Genetics
Genetics

Reputation: 301

Looping through a set of files linux based on filepath

I have directory with lots of compressed data with with a couple of file names. I have two file types als.sumstats.lmm.chr and als.sumstats.meta.chr. After chr there is a number 1-22. I want to loop through only the als.sumstats.meta.chr. However, my code is not working. I keep getting gzip: /ALSsummaryGWAS/Summary_Statistics_GWAS_2016/als.sumstats.meta.chr*.txt.gz: no such file or directory, suggesting my files are not being found with my loop. Can someone help. This is what I have right now.

#!/bin/bash

FILES=/ALSsummaryGWAS/Summary_Statistics_GWAS_2016/als.sumstats.meta.chr*.txt.gz
for f in $FILES;
do
 echo "$FILES"
 echo "extracting columns 2,1,3,9"
 gunzip -c $f | awk '{print $2, $1, $3, $14+$15}' >> ALSGWAS.txt
done

Upvotes: 0

Views: 32

Answers (1)

Zahid Adeel
Zahid Adeel

Reputation: 288

In your script snippet, wildcard '*' pattern is stored as a string in the $FILES variable which needs to be evaluated at some point to get the list of matching files.

In order to evaluate it, you can use eval like this:

FILES="ls -1 /ALSsummaryGWAS/Summary_Statistics_GWAS_2016/als.sumstats.meta.chr*.txt.gz"
for f in $(eval $FILES);
do
    echo "$FILES"
    echo "processing $f"
    echo "extracting columns 2,1,3,9"
    gunzip -c $f | awk '{print $2, $1, $3, $14+$15}' >> ALSGWAS.txt
done

But eval is not a recommended way to do such operations (eval is dangerous), so you can try it like this:

FILES=$(ls -1 /ALSsummaryGWAS/Summary_Statistics_GWAS_2016/als.sumstats.meta.chr*.txt.gz)
for f in $FILES;      
do
    echo "$FILES"
    echo "processing $f"
    echo "extracting columns 2,1,3,9"
    gunzip -c $f | awk '{print $2, $1, $3, $14+$15}' >> ALSGWAS.txt
done

Upvotes: 1

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