DeepRank / 3D-Vac

Personalized cancer vaccine design through 3D modelling boosted geometric learning.
Apache License 2.0
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Structure data folder #43

Closed gcroci2 closed 1 year ago

gcroci2 commented 2 years ago

We started symlinking data on Snellius with folders on 3D-Vac repo, but it was a bit messy and at the end we didn't finish the job.

For now, we're going to keep the exact data structure that we have on Snellius, soft linking data. See issue #47

In the future, we're probably going to restructure it in something like this:

├── data
│   │
│   ├── hdf5
│   │   ├── cnn         <- hdf5 files generated with old version of deeprank, for cnns training
│   │   └── gnn         <- hdf5 files generated with new version of deeprank, for gnns training
│   │
│   ├── 3d_models       <- aligned 3d models, output of pandora
│   │
│   ├── external
│   │   ├── processed   <- csv files ready for the modelling
│   │   └── unprocessed <- BA and EL text data (csv)
│   │
│   └── pssm
│       ├── mapped
│       ├── unmapped
│       └── blast_dbs   <- blast databases and MSAs to generate them
gcroci2 commented 1 year ago

This is outdated. In case in which we'll change the snellius data structure again we'll open a new issue.