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Normalize-by-median.py script as a module #1901

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zmunro opened this issue Dec 17, 2019 · 1 comment
Open

Normalize-by-median.py script as a module #1901

zmunro opened this issue Dec 17, 2019 · 1 comment

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@zmunro
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zmunro commented Dec 17, 2019

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?

@standage
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This has been a pain point for...a while. See #389 (comment). 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.

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