/ec-number-prediction

Using similarity in embedding space for predicting EC numbers

Primary LanguageJupyter Notebook

Readme.md

Getting started

To install the 'ProtPred' environment from environment.yml run:

conda env create -f environment.yml
conda activate ProtPred

Folder structure

The following Folder structure is expected:

├── data
│   ├── annotations
│   │   └── merged_anno.txt
│   ├── ec_vs_NOec_pide100_c50.h5
│   ├── lookupSets
│   │   ├── ec_vs_NOec_pide100_c50.fasta
│   │   ├── ec_vs_NOec_pide20_c50_test.fasta
│   │   ├── ec_vs_NOec_pide20_c50_train.fasta
│   │   ├── ec_vs_NOec_pide20_c50_val.fasta
│   │   ├── ec_vs_NOec_pide30_c50.fasta
│   │   ├── ec_vs_NOec_pide40_c50.fasta
│   │   ├── ec_vs_NOec_pide50_c50.fasta
│   │   ├── ec_vs_NOec_pide60_c50.fasta
│   │   ├── ec_vs_NOec_pide70_c50.fasta
│   │   ├── ec_vs_NOec_pide80_c50.fasta
│   │   └── ec_vs_NOec_pide90_c50.fasta
│   └── nonRed_dataset.tar.gz
├── data_stats.py
├── environment.yml
├── h5opener.py
├── readme.md
├── Simple_data_exploration.ipynb
├── Untitled.ipynb
└── utils.py