extracting segments from .qual file
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.
1 answer
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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Ram
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Matt Shirley
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