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Add verification that sequence looks like sequence #5

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DavidEHufnagel opened this issue Dec 20, 2024 · 3 comments
Open

Add verification that sequence looks like sequence #5

DavidEHufnagel opened this issue Dec 20, 2024 · 3 comments

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@DavidEHufnagel
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Inside fasta_manager, when a FastaEntry is created it should first check that the sequence looks like sequence, meaning that it is in one of these categories:

  1. Is a standard nucleotide base: 'A','T','C','G'
  2. Is a nonstandard nucleotide base representing multiple possibilities like 'Y'
  3. Represents a lack of data properly with a '-' or an 'N'
@sammysheep
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This functionality does exist in Zoe as well, but no harm in doing it yourself.

@DavidEHufnagel
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I thought Zoe would be good at this. We discussed that Zoe is not public, which is when I considered implementing it personally. That's a barrier to using Zoe. I'm less concerned about having to adopt nightly. If you have a timeline for Zoe I'd like to hear it either in this venue or elsewhere. I'm sure it's also generally worthwhile to consider whether adding a dependency could work well to save development time.

@DavidEHufnagel DavidEHufnagel assigned akim135 and unassigned akim135 Jan 6, 2025
@DavidEHufnagel
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Add to the list here to ensure that the sequence is not empty

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