Kipoi 0.6 release notes

Major updates

Hosting models on zenodo/figshare instead of Git-LFS

Kipoiseq — standard dataloaders for sequence-based models

  • dataloaders — Final object used to train models and make predictions. Example: SeqIntervalDl, MMSpliceDl.
  • transforms — simple functions or callable classes that for example resize the genomic intervals or one-hot-encode the DNA sequence
  • extractors — given a genomic interval, extract the values from genome-wide files like FASTA or BigWig. See also genomelake for more extractors.

Contributing multiple very similar models with a template

  • model-template.yaml — template for model.yaml
  • models.tsv — tab-separated files holding custom model variables
First few lines of model-template.yaml.
First few lines of models.tsv.

Prediction testing

Common conda environments

Minor updates

  • Add kipoi get-example command.
  • Allow to parametrize custom models PR#245
  • Keep track of the kipoi version required for the models source and display a warning if it has to be updated PR #377
  • Allow to read yaml files with additional fields using the old kipoi version (e.g. only display a warning)
  • Add option to disable automatic updates of the model repository. Use auto_update: False in ~/.kipoi/config.yaml.

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