Add unique Output files names with loop in linux/bash

Question

I have 96 bam files, How do I output the txt file with the unique sample IDs? I am looping through the bam files, but need to assign unique output files. For example: SC845414.txt

#Typical Bam Files:
SC845414-CTGATCGT-GCGCATAT_Aligned.sortedByCoord.out.bam
SC845425-TGTGACTG-AGCCTATC_Aligned.sortedByCoord.out.bam

#!/bin/bash
#SBATCH --mem=110g
#SBATCH --cpus-per-task=12
#SBATCH --time=10-00:00:00

module load python

DIR=/PATH/*

for d in $DIR; do
    python -m HTSeq.scripts.count -s yes -f bam "$d" /PATH1/gencode.v35.annotation.gtf > /PATH3/HTseq/SC845414.txt
done

Nick S · Accepted Answer · 2022-11-17 18:47:05Z

1

It depends highly on what exactly you mean by "sample ID".

Based on your example, if you mean "the part of the filename before the first dash", then you could do this:

for d in $DIR; do
    id=$(basename "$d" | cut -f 1 -d -)
    python -m HTSeq.scripts.count -s yes -f bam "$d" /PATH1/gencode.v35.annotation.gtf > "/PATH3/HTseq/$id.txt"
done

edited Nov 17, 2022 at 18:47

answered Nov 17, 2022 at 17:16

Nick S

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9 Comments

Genetics Over a year ago

Why is thre "" around this? "/PATH3/HTseq/$id.txt" and not just "id"?

Nick S Over a year ago

You need the $ to make it a variable, so it needs to be $id, not id. And it's a good idea to quote anything with a variable in it, for several reasons (see here). Well, unless you're relying on features that don't work in quotes (like your use of $DIR where you expect the * to be expanded).

Genetics Over a year ago

This is what I am getting:

Genetics Over a year ago

DIR=/P/A/T/T/SC915966-GCGTCATT-CAGACGTT_Aligned.sortedByCoord.out.bam

Genetics Over a year ago

id=$(printf '%s' "$DIR" | cut -f 1 -d -)

|

tomc · Accepted Answer · 2022-11-17 20:48:59Z

0

same; but using builtin variable interpolation instead of calling basename and cut

for d in $DIR; do
    fname=${d##*/}
    python -m HTSeq.scripts.count -s yes -f bam "$d" /PATH1/gencode.v35.annotation.gtf > "/PATH3/HTseq/${fname%%-*}.txt"
done

(edited to strip any leading path as well)

unfortunately stripping both the leading and trailing parts of a variable at once is beyond me (at the moment).

seems it should be do-able see: https://www.thegeekstuff.com/2010/07/bash-string-manipulation/

(no affiliation or endorsement; just first relevant web search)

edited Nov 17, 2022 at 20:48

answered Nov 17, 2022 at 20:04

tomc

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2 Comments

Nick S Over a year ago

Is this sh compatible or just bash?

tomc Over a year ago

bash as far as know, tcsh had some other convention I have since forgotten

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