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I have multiple .GFF files, each in a single directory per annotated whole genome, that I wish to copy into a single directory so that I can perform a core genome alignment.

However the following code does not seem to work:

for pathname in "~/ST_0075/annotations/*/*.gff"; do cp "$pathname" ~/ST_0075/alignment; done

The directory structure is the following:

Home
-ST_0075
---Annotations
-----Sample_001
----------001.gff

The goal is to copy from multiple Sample_XXX subdirectories within Annotations the XXX.gff files into another directory named alignment

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Tinkered a bit and realized the solution did not neccistate a for loop.

mkdir ~/ST_0075/alignment; cp ~/ST_0075/annotations/*/*.gff ~/ST_0075/alignment
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    $\begingroup$ Exactly, and thanks for posting an answer! Note that if you're using bash, you can make it even simpler if you enable globstar. You can do: shopt -s globstar; cp ~/ST_0075/annotations/**/*.gff ~/ST_0075/alignment and that will recurse an arbitrary number of directories under annotations, so you don't need to count the exact number of */ you need. $\endgroup$
    – terdon
    Jul 12 at 16:59
  • $\begingroup$ Hi @terdon, is it ** that is doing the trick? $\endgroup$
    – haci
    Jul 12 at 17:52
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    $\begingroup$ Yes, try man bash | grep -A3 'globstar$' to see the details. $\endgroup$
    – terdon
    Jul 12 at 17:56

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