├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── docker-compose.yml ├── envs ├── cpu.yml ├── gpu.yml └── kmc.yml ├── img ├── panspace-app.gif ├── panspace-logo-v5.png ├── panspace-pipeline.png └── panspace-query.png ├── notebooks ├── 01-metrics-test-index.ipynb ├── 02-outliers-and-missclasified.ipynb ├── 03-UMAP-FCGR.ipynb ├── 03-confident-learning.ipynb ├── autoencoder-imgs.ipynb ├── balance_triplet_batches.ipynb ├── create_jpeg.ipynb ├── cross-validation-metrics.ipynb ├── cross-validation-mislabeled_.ipynb ├── cross-validation-ood_.ipynb ├── distances-embeddings.ipynb ├── dustbin-files.ipynb ├── interpolate-embeddings.ipynb ├── logs_fcgr_pipeline.ipynb ├── phoenix.ipynb ├── plot-fcgr-masks.ipynb ├── plots-FCGR.ipynb ├── plots-stats-assemblies.ipynb ├── test.ipynb ├── train_mlp.ipynb └── use-encoder.ipynb ├── pyproject.toml ├── scripts ├── config_fcgr.yml ├── config_query.yml ├── download_allthebacteria.sh ├── envs │ ├── cpu.yml │ ├── gpu.yml │ └── kmc.yml ├── fcgr_allthebacteria.smk ├── fcgr_plain_fa.gz_allthebacteria.smk ├── fcgr_plain_fasta_allthebacteria.smk ├── query.smk ├── query_fast.smk └── smk_batches.sh ├── sequences ├── SAMD00157547.fa.gz ├── SAMEA2609553.fa.gz ├── SAMEA747610.fa └── SAMEA800338.fna └── src └── panspace ├── __init__.py ├── data_curation.py ├── dataclasses_cli ├── __init__.py ├── activation.py ├── autoencoder.py ├── loss.py ├── metric_learning.py ├── optimizer.py └── preprocessing.py ├── dnn ├── __init__.py ├── callbacks.py ├── loaders │ ├── __init__.py │ ├── autoencoder.py │ ├── generator_batches.py │ ├── metric_learning.py │ └── utils.py ├── models │ ├── __init__.py │ ├── autoencoder_fcgr.py │ ├── cnn_fcgr.py │ ├── cnn_fcgr_dropout.py │ ├── cnn_fcgr_levels.py │ ├── custom_layers │ │ ├── __init__.py │ │ ├── conv_fcgr.py │ │ ├── deconv_fcgr.py │ │ └── euclidean_distance.py │ └── resnet50.py └── utils │ ├── __init__.py │ ├── split_data.py │ └── split_data_cross_validation.py ├── fcgr.py ├── fcgr_mods ├── __init__.py ├── fcgr_from_kmc.py ├── fcgr_from_tar.py └── fcgr_modified.py ├── index.py ├── panspace.py ├── pipelines ├── envs │ ├── cpu.yml │ ├── gpu.yml │ └── kmc.yml ├── query.smk └── query_fast.smk ├── stats_assembly.py ├── streamlit ├── __init__.py ├── app.py ├── ena.py ├── html.py ├── interactive_plot.py └── utils.py ├── trainer.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pg-space/panspace/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pg-space/panspace/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pg-space/panspace/HEAD/LICENSE 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