Treatment

Notes taken for the organization of the DBGI pilot MS data for its intake as a graph.

Export of the minimal required files

• mgf
• quant table
• mgf sirius

Starting from the mzmine project

use th /media/share/DBGI/{} following pattern to export with the original filename

python script availabl at

https://github.com/mandelbrot-project/indifiles_annotation/blob/main/organization/rename_pos.py

Maybe bash command line could be more flexible. Let's try

We inspire from https://stackoverflow.com/a/10536148

for file in prefix*; do mv "$file" "${file#XY TD-}" done

and adapt (note we echo first for safety)

for file in 20220513PMA*; do echo mv "$file" "${file##20220513PMA}" done

Seems to work

So we can

for file in 20220513PMA*; do mv "$file" "${file##20220513PMA}" done

Now we are left with the extensions We inspire from

Rename all .txt to .text

for f in *.txt; do mv -- "$f" "${f%.txt}.text" done

And adapt to

for f in *.mzML_chromatograms_deconvoluted_deisotoped.mgf; do mv -- "$f" "${f%.mzML_chromatograms_deconvoluted_deisotoped.mgf}_sirius_pos.mgf" done

and

for f in *.mzML_chromatograms_deconvoluted_deisotoped_quant.csv; do mv -- "$f" "${f%.mzML_chromatograms_deconvoluted_deisotoped_quant.csv}_features_quant_pos.csv" done

Now we are left with mgf (sirius and classical) We will use pattern expansion to limit our suffix editing

ls DBGI01_04{001..100}_sirius_pos.mgf

In fact its easier to mv all file with the sirius_pos.mg extension to a temp folder mv *sirius_pos.mgf sirius Do the substitution

for f in *.mgf; do mv -- "$f" "${f%.mgf}_features_ms2_pos.mgf" done

Now that we have our file we would like to create subfolder for them and move them accordingly

https://unix.stackexchange.com/a/485309

Adapted for i in ls -ltrh directorypath| awk '{print $NF}'| awk -F "_f|_s" '{print $1}'| sort| uniq; do mkdir $i; yes|mv $i* $i; done

Works nicely !