ENH: allow passing MAGs to the compute action #7
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Hey @ctb, these are some changes that @nbokulich mentioned to you - do you think you could have a look? 🙏 |
ctb
reviewed
Aug 17, 2023
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| command = ['sourmash', 'compute', str(output) + "/*", '--ksizes', str(ksizes), '--scaled', str(scaled)] | ||
| command = [ | ||
| 'sourmash', 'compute', f'{output}/*', |
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in our next major release of sourmash, sourmash v5, we will be removing sourmash compute per sourmash-bio/sourmash#1286.
It's been replaced with sourmash sketch; the following should work:
ksizestr = [ f"k={k}" for k in ksizes ]
ksizestr = ",".join(ksizestr)
abundstr = "noabund"
if track_abundance:
abundstr = "abund"
command = ['sourmash', 'sketch', 'dna', f'{output}/*', '-p', f'scaled={scaled},{ksizestr},{abundstr}'
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Good to know, thanks for info! Should we then update it in a separate PR, once v5 is out?
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Commented in one place - and overall looks good to me. Should I approve in review & merge? |
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That would be lovely, thanks! |
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This PR adds an ability to pass MAG sequences to the
computeaction, so that the MinHash signatures can also be computed for this kind of DNA sequences.