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Modify Annotation to allow for multiple seq #42

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NickleDave opened this issue Jul 17, 2019 · 2 comments · Fixed by #243
Closed

Modify Annotation to allow for multiple seq #42

NickleDave opened this issue Jul 17, 2019 · 2 comments · Fixed by #243
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ENH: enhancement New feature or request
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@NickleDave
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NickleDave commented Jul 17, 2019

Stack module was added but yes, looks like we're not using it?

Not sure now if we should be. Leaving this open

@NickleDave NickleDave added this to In Progress in 2.1.0 Jul 17, 2019
@NickleDave NickleDave removed this from In Progress in 2.1.0 Jan 3, 2021
@NickleDave NickleDave added the ENH: enhancement New feature or request label Dec 2, 2021
@NickleDave NickleDave self-assigned this Mar 28, 2022
@NickleDave NickleDave added this to To do in ENH Mar 20, 2023
@NickleDave NickleDave changed the title actually use Stack with Annotations, e.g. with TextGrids Modify Annotation to allow for mulitple seq Mar 20, 2023
@NickleDave NickleDave changed the title Modify Annotation to allow for mulitple seq Modify Annotation to allow for multiple seq Mar 20, 2023
@NickleDave
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Changing the issue name but bringing it back to life.

We want to be able to handle TextGrids with multiple tiers.
See discussion here:
pyOpenSci/software-submission#68 (comment)

Need to look at the right way to implement this.

Can we just allow Seq to be either a single Sequence or a list of Sequences?
Not clear to me how much hierarchy are allowed by Tiers in TextGrids.

@NickleDave
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Thinking about this more, a quick fix for now I think will be to do the following:

  • add a new attribute seqs which is a Python tuple of crowsetta.Sequences
  • for seq-like formats that only ever have a single seq
  • for formats that can have multiple seqs per annotation file, such as TextGrid, they can be converted to an annotation with multiple sequences

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