New notebook dealing with metagenomics FASTA files
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Notebook idea
- Dominant language
- Jupyter Notebook
- Stars
- 16
- Forks
- 15
- Avg merge
- 1h 39m
- Merged PRs (30d)
- 6
Description
- What is language(s) for used in the example?
- Python
- Is it focused on a particular module/software or an IOOS data service?
- FASTA file format, parquet format, and Dask
- Can you provide a minimum example of the expected code and results in a notebook?
- See the notebooks in https://github.com/jonathancosme/COSME/tree/master/notebook_walkthroughs, especially A_convert_raw_to_parquet.ipynb.
Description of the notebook:
Folks are starting to do more work with metagenomics data in python. Jonathan Cosme (Deloitte) has written a few notebooks (linked above) that we should explore porting to the CodeLab. I like the first notebook as it converts raw FASTA files to parquet for manipulation in AI/ML techniques.
CC: @hmoustahfid-NOAA
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the linked COSME notebooks, especially A_convert_raw_to_parquet.ipynb, and compare their approach with existing notebooks in this repository. Port the FASTA-to-parquet workflow into a new CodeLab notebook, with the expected example code and results demonstrated.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- data-engineering, machine-learning
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100