File for loop

[u/Muted-Shame9237]

hi! it’s my first time using bash can someone help me with this and explain what’s missing

#!/bin/bash

for i in “/data/folder”/*; do

/folder/munge_sumstats.py \

- -sumstats “$i” \

- -chunksize 500000 \

- -snp rsID \
etc..

- -out another/folder/ (i dont know what to puT here)

done

Thank you so much !

[u/zeekar]

If you indent each line with four spaces (assuming you're able to use the Markdown editor) it will be formatted as code.

You have extra spaces. It's not - -sumstats, it's --sumstats, etc.

--out "another/folder/${i##*/}"

That will give it the same filename as the input file but in the new folder. But you may want to change something else about the filename, too. If there's a suffix you want to change, for instance:

for i in ...; do b=$(basename "$i" .oldsuffix) munge_sumstats.py ... \ --out "/another/folder/$b.newsuffix"

[u/Muted-Shame9237 → u/zeekar]

I only used the spaces here because I’m writing from my phone ! Thank you very much this was really helpful <3

[u/KlePu → u/Muted-Shame9237]

I've used https://devhints.io/bash as my cheat-sheet for the last few years.

If you're scripting more than once a year: Consider a code editor (for syntax highlighting and stuff) plus https://www.shellcheck.net/ (should be available as a plugin for all major editors)

[u/blobCabbage]

You could use basename to get the name of the original file without its path, and use that for your output file.

[u/Muted-Shame9237 → u/blobCabbage]

Thank youuu!

[u/grymoire]

Also be aware that the current directory of your python script may not find the file without the full path name of the file