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extracting segments from .qual file
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3.7 years ago
Stephen • 10
Ireland

Is there anything similar to _getfasta _(bedtools) but will also work on an associated .qual file in the format:

    >Scaff3
    50 50 50 50 50 40 40 40 30 30 30 34 34 34 34

I basically need to extract a list of specific segments from the .qual file, and wondering if anyone knows of a suitable tool already available.

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Entering edit mode
14 months ago
Cambridge, MA

You can use pyfaidx for this:

pip install (--user) pyfaidx
faidx scaffolds.qual Scaff3:1-8 Scaff3:4-11
>Scaff3:1-8
50 50 50
>Scaff3:4-11
50 50 50

Since a "qual" file has 3 characters per position, just make sure you count in threes to preserve your formatting.

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