I looked all day from tutorials to ready made bash scripts, but couldn't find what I need. Also I never wrote a bash script before... :/

Here's my problem (to quote from full metal jacket: "there are many like it, but this one is mine"): I have a directory with 120 files that come in triplets (in bold I marked what's unique to every file triplet): GSM6025613_SJWLM030043_D1_barcodes.tsv
GSM6025613_SJWLM030043_D1_features.tsv
GSM6025613_SJWLM030043_D1_matrix.mtx

GSM6025615_SJWLM071563_D1_barcodes.tsv
GSM6025615_SJWLM071563_D1_features.tsv
GSM6025615_SJWLM071563_D1_matrix.mtx

...

I would like to have a bash script that creates new directories with names according to the triplets unique strings (f.e. '613', '615') moves the three corresponding files (*barcode.tsv, *features.tsv, *matrix.mtx) to the corresponding directory and renames them so that the files are just called "barcode.tsv", "features.tsv" and "matrix.mtx".

I tried it with a for loop, but I'm pretty blank on bash scripting and beyond the second line, honestly, it's all jibberish to me (for now)... :/

#!/bin/bash for f in *.{tsv,mtx} do ... done

I appreciate any help!

CodePudding user response：

You can use sed to split the file name into its components, something like this

file='GSM6025615_SJWLM071563_D1_barcodes.tsv'
eval $(sed -E 's/(GSM....)([0-9] )_(.*)_(.*)_(.*)\.tsv/n=\2;f=\5;/' <<< "$file")
echo $n
615
echo $f
barcodes

eval allows you to take the output of sed (the n and f variable assignments) and convert it to variables.

CodePudding user response：

Try this Shellcheck-clean code (maybe on a copy of your directory first!):

#! /bin/bash -p

shopt -s nullglob

for file in GSM6025[0-9][0-9][0-9]_*_{features.tsv,matrix.mtx,barcodes.tsv}
do 
    dir=${file#GSM6025}
    dir=${dir%%_*}

    newfile=${file##*_}

    mkdir -p -v -- "$dir"
    mv -n -v -- "$file" "$dir/$newfile"
done

• shopt -s nullglob makes globs expand to nothing when nothing matches (otherwise they expand to the glob pattern itself, which is almost never useful in programs).
• See Removing part of a string (BashFAQ/100 (How do I do string manipulation in bash?)) for explanations of ${file#GSM6025} etc.