license:other region:us
@article{Goodstein2011,
  doi = {10.1093/nar/gkr944},
  url = {https://doi.org/10.1093/nar/gkr944},
  year = {2011},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {40},
  number = {D1},
  pages = {D1178--D1186},
  author = {David M. Goodstein and Shengqiang Shu and Russell Howson and Rochak Neupane and Richard D. Hayes and Joni Fazo and Therese Mitros and William Dirks and Uffe Hellsten and Nicholas Putnam and Daniel S. Rokhsar},
  title = {Phytozome: a comparative platform for green plant genomics},
  journal = {Nucleic Acids Research}
}
---
license: other
---

# Phytozome Genomes

This dataset consists of 100 current (as of 2023-06-20) _unrestricted_
Phytozome genome assemblies, listed in `genomes.tsv`.

Currently, the training, validation, and test splits are a random
90/5/5% split, but this will change before version 1.0.

Individual observations are entire chromosomes/contigs, so it is up to
the user to chunk them up further to their appropriate size.

## Quickstart

```
$ conda env create --file environment.yml
$ conda activate phytozome_genomes_dataset
```

```python
import datasets
dataset = datasets.load_dataset('twrightsman/phytozome_genomes', username = 'my_jgi_username', password = 'my_jgi_password')
for observation in dataset['train']:
    # do cool stuff here, for example:
    seqid = observation['seqid']
    sequence = observation['sequence']
```
