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Add Jupyter notebook examples / autometa code snippets #214

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evanroyrees opened this issue Jan 7, 2022 · 0 comments
Open
5 tasks

Add Jupyter notebook examples / autometa code snippets #214

evanroyrees opened this issue Jan 7, 2022 · 0 comments
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documentation Improvements or additions to documentation good first issue Good for newcomers

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@evanroyrees
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evanroyrees commented Jan 7, 2022

I think it may be helpful to throw an example into Jupyter notebook and link to it (or https://docs.readthedocs.io/en/stable/guides/jupyter.html)
Especially since the tutorial jumps around between running things on command line and python

  • Benchmarking Example
  • Exploring a metagenome/binning using Autometa imports

Additional code snippets could be added using the autometa api located on autometa.readthedocs.io under Autometa python API

  • Quickly determining a set of contigs' bin metrics
  • Quickly retrieving a set of taxids lineages (including both canonical and non-canonical ranks)
  • Some parameter sweep workflows regarding kmers or binning (maybe tying in benchmarking from above?)

Originally posted by @chasemc in #189 (comment)

@evanroyrees evanroyrees changed the title I think it may be helpful to throw an example into Jupyter notebook and link to it (or https://docs.readthedocs.io/en/stable/guides/jupyter.html) I think it may be helpful to throw an example into Jupyter notebook and link to it Jan 7, 2022
@evanroyrees evanroyrees changed the title I think it may be helpful to throw an example into Jupyter notebook and link to it Add Jupyter notebook examples Jan 7, 2022
@evanroyrees evanroyrees added the documentation Improvements or additions to documentation label Jan 7, 2022
@evanroyrees evanroyrees changed the title Add Jupyter notebook examples Add Jupyter notebook examples / autometa code snippets Jan 27, 2022
@chasemc chasemc added the enhancement New feature or request label Feb 8, 2022
@evanroyrees evanroyrees added good first issue Good for newcomers and removed enhancement New feature or request labels Feb 18, 2022
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Labels
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