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Asked: 2026-05-31T18:45:31+00:00

I have one folder with about 1000 files and I want to group them

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I have one folder with about 1000 files and I want to group them according to their resepctive parent folders.

I did ls- R > updated.txt to get the original setup of folders and files.

The updated. txt looks like this:

./Rhodococcus_RHA1:
NC_008268.fna
NC_008269.fna
NC_008270.fna
NC_008271.fna

./Rhodoferax_ferrireducens_T118:
NC_007901.fna
NC_007908.fna

./Rhodopseudomonas_palustris_BisA53:
NC_008435.fna

./Rhodopseudomonas_palustris_BisB18:
NC_007925.fna

./Rhodopseudomonas_palustris_BisB5:
NC_007958.fna

./Rhodopseudomonas_palustris_CGA009:
NC_005296.fna
NC_005297.fna

So, by looking at this file, I know what files go into what folder. The folder with all the 1000 files together looks like this:

results_NC_004193.fna.1.ebwt.map
results_NC_004307.fna.1.ebwt.map
results_NC_004310.fna.1.ebwt.map
results_NC_004311.fna.1.ebwt.map
results_NC_004337.fna.1.ebwt.map
results_NC_004342.fna.1.ebwt.map
results_NC_004343.fna.1.ebwt.map
results_NC_004344.fna.1.ebwt.map

and so on…

You can see that the filenames of all the 1000 files are dependent on their original names in the folder setup(if that’s a good way to explain it).

I want to move these results_XXXXXXXX files to folders (have to create new folders) with the original setup. So it should be something like this:

./Rhodococcus_RHA1: (this is a folder)
results_NC_008268.fna.1.ebwt.map 
results_NC_008269.fna.1.ebwt.map
results_NC_008270.fna.1.ebwt.map
results_NC_008271.fna.1.ebwt.map

./Rhodoferax_ferrireducens_T118:
results_NC_007901.fna.1.ebwt.map
results_NC_007908.fna.1.ebwt.map

I don’t really know how to do this… maybe some kind of mov command? I’d appreciate help with this problem.

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1 Answer

  1. Editorial Team

    Run the following command from the folder where you have those 1000 files. The path/to/original/files is the path to the original files (the one that you did ls -R). you should get a list of mv commands. Verify several of them to confirm that those are correct. If so, add | sh next the command and rerun it to execute those commands. If you don’t have all the corresponding files in the 1000 files folder, you would get mv commands that would return “file not found”, that can be ignored or piped to /dev/null. This assumes that you always have a file in original folder so that it knows where to move the file. If not, some of those 1000 files won’t be moved. As always, take a good backup before you do this.

    find path/to/original/files -type f | awk -F"/" '{ path=$0; sub($NF, "", path); printf("mv results_%s.1.ebwt.map \"%s\"\n", $NF, path);}'
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