khmer
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Normalize-by-median.py script as a module
The normalize-by-median.py
script (under /scripts) would be very useful as a module. I want to be able to do something like:
import khmer
khmer.normalize_by_median(input=fastqgz_filepath, output=output_fastqgz)
Is something like this already possible?
This has been a pain point for...a while. See https://github.com/dib-lab/khmer/issues/389#issuecomment-63123529. This was planned for khmer (to be renamed as oxli) version 3.0, which unfortunately never really materialized. I don't anticipate that this will be supported, at least any time soon. I've heard hints that khmer/oxli may be rebooted soon.