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One input fasta class bug #34

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biodataganache opened this issue Dec 16, 2021 · 2 comments
Open

One input fasta class bug #34

biodataganache opened this issue Dec 16, 2021 · 2 comments
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@christinehc
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bug Something isn't working enhancement New feature or request

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@biodataganache
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A common application of Snekmer model mode might be to build a model based on a single input fasta file using another fasta file as background (i.e. the other class). Currently this fails. We should detect if this configuration is present (one fasta file as input and one as background) and consider it to be a binary classification problem.
@biodataganache biodataganache added bug Something isn't working enhancement New feature or request labels Dec 16, 2021
@christinehc
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Referenced in #13

@christinehc christinehc self-assigned this Dec 16, 2021
@biodataganache
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It's similar to the issue described in #13 but distinct - #13 talks about problems with a file containing one sequence, this issue is about a run containing one class (that might have a lot of sequences)

christinehc added a commit that referenced this issue Mar 16, 2022
@christinehc
Remove old files. Create output files for demo. Fixes #28, #36
c4ed9d8 
Outdated example files have been removed and the example folder renamed to reflect its contents of purely data. All output files have been created for the demo notebook for the user to gain familiarity with the output files created by Snekmer.

The demo notebook has been updated to more closely reflect the `snekmer search` code, and the section renamed accordingly. The scoring section has also been slightly modified to create the same output files/directories as snekmer.

Also addresses #34.
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@biodataganache @christinehc