├── .gitignore ├── .lgtm.yml ├── .readthedocs.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── data ├── README.md ├── encoding_example.txt ├── nucleotide_dataset.tsv ├── nucleotide_encoding.txt ├── res_class_dataset.tsv ├── res_regress_dataset.tsv ├── seq_class_dataset.tsv ├── seq_regress_dataset.tsv ├── seqfile.txt ├── seqfile_noIDs.txt └── splitfile.txt ├── devtools ├── README.md ├── conda-envs │ └── test_env.yaml ├── scripts │ └── create_conda_env.py └── travis-ci │ └── before_install.sh ├── docs ├── Makefile ├── README.md ├── _build │ ├── doctrees │ │ ├── api.doctree │ │ ├── environment.pickle │ │ ├── getting_started.doctree │ │ ├── index.doctree │ │ ├── modules │ │ │ └── train_network.doctree │ │ └── usage │ │ │ ├── brnn_optimize.doctree │ │ │ ├── brnn_predict.doctree │ │ │ ├── brnn_train.doctree │ │ │ ├── examples.doctree │ │ │ ├── ml_faqs.doctree │ │ │ ├── optimize.doctree │ │ │ ├── parrot-optimize.doctree │ │ │ ├── parrot-predict.doctree │ │ │ ├── parrot-train.doctree │ │ │ ├── predict.doctree │ │ │ ├── quickstart.doctree │ │ │ └── train.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ ├── brnn_diagram.png │ │ ├── res_CM.png │ │ ├── res_scatter.png │ │ ├── seq_CM.png │ │ ├── seq_scatter.png │ │ └── train_test.png │ │ ├── _modules │ │ ├── index.html │ │ ├── parrot │ │ │ ├── bayesian_optimization.html │ │ │ ├── brnn_architecture.html │ │ │ ├── brnn_plot.html │ │ │ ├── encode_sequence.html │ │ │ ├── process_input_data.html │ │ │ └── train_network.html │ │ └── prot_brnn │ │ │ ├── bayesian_optimization.html │ │ │ ├── brnn_architecture.html │ │ │ ├── brnn_plot.html │ │ │ ├── encode_sequence.html │ │ │ ├── process_input_data.html │ │ │ └── train_network.html │ │ ├── _sources │ │ ├── api.rst.txt │ │ ├── getting_started.rst.txt │ │ ├── index.rst.txt │ │ ├── modules │ │ │ └── train_network.rst.txt │ │ └── usage │ │ │ ├── brnn_optimize.rst.txt │ │ │ ├── brnn_predict.rst.txt │ │ │ ├── brnn_train.rst.txt │ │ │ ├── examples.rst.txt │ │ │ ├── ml_faqs.rst.txt │ │ │ ├── optimize.rst.txt │ │ │ ├── parrot-optimize.rst.txt │ │ │ ├── parrot-predict.rst.txt │ │ │ ├── parrot-train.rst.txt │ │ │ ├── predict.rst.txt │ │ │ ├── quickstart.rst.txt │ │ │ └── train.rst.txt │ │ ├── _static │ │ ├── README.md │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Inconsolata.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── api.html │ │ ├── genindex.html │ │ ├── getting_started.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── usage │ │ ├── ml_faqs.html │ │ ├── parrot-optimize.html │ │ ├── parrot-predict.html │ │ └── parrot-train.html ├── _static │ └── README.md ├── _templates │ └── README.md ├── api.rst ├── conf.py ├── getting_started.rst ├── images │ ├── brnn_diagram.png │ ├── combined_CV_test_scatter.png │ ├── res_class_network_res_CM.png │ ├── res_regress_network_res_scatterplot.png │ ├── separate_CV_test_scatter.png │ ├── seq_class_network_seq_CM.png │ ├── seq_class_network_train_val_loss.png │ └── seq_regress_network_seq_scatterplot.png ├── index.rst ├── make.bat ├── requirements.txt └── usage │ ├── advanced_examples.rst │ ├── basic_examples.rst │ ├── cross_validation.rst │ ├── ml_faqs.rst │ ├── parrot-cvsplit.rst │ ├── parrot-optimize.rst │ ├── parrot-predict.rst │ └── parrot-train.rst ├── idptools_parrot.egg-info ├── SOURCES.txt ├── dependency_links.txt ├── not-zip-safe ├── requires.txt └── top_level.txt ├── parrot ├── __init__.py ├── 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