CODEWITHSUNDEEP
bashloops
Genetics
Genetics

Reputation: 301

How to get a unique output file for each loop with bash

I have a script below, I am looping throught GTEx brain tissues and running a program laid out below. How do I in the --output put a unique output file? I am lost on this, still kind of new to bash. BTW, TISSUE files look like this: Brain_Frontal_Cortex_BA9.genes.annot and Lung.genes.annot In the GTExV8 folder, I have 48 unique files that TISSUE will loop through. Thus, the output for one example would be Brain_Frontal_Cortex_BA9_emagma and Lung_emagma

#!/bin/bash

for TISSUE in GTExV8/*;
do
./magma 
--bfile g1000_eur 
--gene-annot $TISSUE 
--pval Summary_Statistics_GWAS_2016/ALSGWAS.txt ncol=Ne 
--gene-settings adap-permp=10000 
--out LABEL WITH EACH TISSUE LOOPED
done

Upvotes: 0

Views: 299

Answers (2)

Ted Lyngmo
Ted Lyngmo

Reputation: 117258

Using Parameter Expansion you can extract the part of the $TISSUE variable that you'd like to use in your output filename.

for TISSUE in GTExV8/*;
do
    # remove the directory part:
    outfile="${TISSUE##*/}"

    # remove the file extension:
    outfile="${outfile%%.genes.annot}"

    # add a filename ending:
    outfile="${outfile}_emagma"

    # use $outfile:
    ./magma ... --gene-annot "$TISSUE" --out "$outfile"
done

Upvotes: 2

Diego Torres Milano
Diego Torres Milano

Reputation: 69198

No sure what you mean, but if your intention is to generate different names for the --out files based on the $tissue file name, and assuming BA9 is the variable part and you want to name the output after it, you can do

#!/bin/bash
for tissue in GTExV8/*;
do
IFS='_.' a=( $tissue )
./magma \
--bfile g1000_eur \
--gene-annot $tissue \
--pval Summary_Statistics_GWAS_2016/ALSGWAS.txt ncol=Ne \
--gene-settings adap-permp=10000 \
--out Amygdala_emagma_${a[3]}
done

which is splitting the $tissue name in an array a to get ${a[3]}

Upvotes: 0

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