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

Question

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

Hi Ted, Could you add an example below. I have 48 tissues with variable names like Brain_Frontal_Cortex_BA9.genes.annot and Lung.genes.annot. Would your example work? — Genetics, Aug 04 '20 at 05:54
Hi Ted, I fixed this, sorry for the confusion. I want to loop through each tissue file, and extract the unique name for my output name in out. — Genetics, Aug 04 '20 at 06:07
Hi Ted, add them to question, I want them to be Brain_Frontal_Cortex_BA9_emagma and Lung_emagma — Genetics, Aug 04 '20 at 06:18
Hi Ted, There are 48 tissues total, I am providing two examples with variable name lengths. Thanks for your help and editing, much better! — Genetics, Aug 04 '20 at 06:26
Do you generally want the string between the last slash and the first dot after it? Please try to state a precise requirement; [edit] your question to keep it self-contained rather than heaping extra information in comments. — tripleee, Aug 04 '20 at 06:29
@Genetics : Why not simply calling the output file `$TISSUE.output`? — user1934428, Aug 04 '20 at 06:31
@Genetics I changed the question to include the example `Lung.genes.annot` instead of `Lung.gene.annot` since I believe you made a typo in the question. I hope that was correct. — Ted Lyngmo, Aug 04 '20 at 06:42

score 2 · Accepted Answer · answered Aug 04 '20 at 06:40

2

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

answered Aug 04 '20 at 06:40

Ted Lyngmo

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1

In case anyone is wondering, `basename` variant of the answer (instead of parameter expansion) is `for TISSUE in GTExV8/*; do ./magma ... --gene-annot "$TISSUE" --out "$(basename "$TISSUE" .genes.annot)_emagma"; done`. But `parameter expansion` is `bash builtin` and hence preferred. `basename` is external executable. – anishsane Aug 04 '20 at 10:54

score 0 · Answer 2 · answered Aug 04 '20 at 05:42

0

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]}

answered Aug 04 '20 at 05:42

Diego Torres Milano

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9
111
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Hi Diego, I think I understand what your example is. The 48 tissues are names differently. Here is another example: Lung.genes.annot. Could this example still work? – Genetics Aug 04 '20 at 05:46
Hi Diego, I would want to extract this whole portion Brain_Frontal_Cortex_BA9 for the output name. – Genetics Aug 04 '20 at 05:51
1

Probably fix the quoting here in case some file names contain shell metacharacters. Keep in mind that your solution should work for future visitors as well, whose requirements may differ from the OP's. See also [When to wrap quotes around a shell variable?](https://stackoverflow.com/questions/10067266/when-to-wrap-quotes-around-a-shell-variable) – tripleee Aug 04 '20 at 06:26

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

2 Answers2