DataSAIL
DataSAIL is a tool to split datasets while reducing information leakage.
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Download Latest Version (.zip)- bug_report.md
- feature_request.md
- question-help-request.md
- detailed_pr_template.md
- fast_pr_template.md
- publish.yaml
- test.yaml
- test_all_pyv.yaml
- test_rdkit.yaml
- cdhit.yaml
- cdhit_est.yaml
- diamond.yaml
- foldseek.yaml
- mash.yaml
- mash_dist.yaml
- mash_sketch.yaml
- mmseqs2.yaml
- mmseqspp.yaml
- __init__.py
- caching.py
- cdhit.py
- cdhit_est.py
- clustering.py
- diamond.py
- ecfp.py
- foldseek.py
- mash.py
- mmseqs2.py
- mmseqspp.py
- tmalign.py
- utils.py
- vectors.py
- wlk.py
- __init__.py
- read.py
- read_genomes.py
- read_molecules.py
- read_other.py
- read_proteins.py
- utils.py
- validate.py
- __init__.py
- cluster_1d.py
- cluster_2d.py
- id_1d.py
- id_2d.py
- overflow.py
- solve.py
- utils.py
- __init__.py
- __main__.py
- argparse_patch.py
- eval.py
- parsers.py
- report.py
- routine.py
- sail.py
- settings.py
- version.py
- asteroids.nblink
- bace.nblink
- pdbbind.nblink
- qm9.nblink
- rna.nblink
- tox21.nblink
- contributing.rst
- metric.rst
- DataSAIL_GCB.png
- DataSAIL_HIPSS.png
- DataSAIL_ISMB.png
- DataSAIL_Logo.png
- DataSAIL_Logo_transparent.png
- DataSAIL_Logo_transparent_4_3.png
- DataSAIL_Logo_transparent_small.png
- mpp.png
- mpp_c1.png
- mpp_i1.png
- phylOverview_splits.png
- pli.png
- PLI_c1.png
- PLI_c1l.png
- PLI_c1p.png
- PLI_c2.png
- PLI_i1.png
- PLI_i1l.png
- PLI_i1p.png
- PLI_i2.png
- PLI_r.png
- Workflow_ICML.png
- cli.rst
- dl_eval.rst
- package.rst
- lppdbbind.html
- moleculenet.html
- pinder.html
- plinder.html
- clustering.rst
- embeddings.rst
- input.rst
- solvers.rst
- splits.rst
- workflow.rst
- conf.py
- faq.rst
- index.rst
- install.html
- Makefile
- other.rst
- posters.rst
- requirements.txt
- asteroids.ipynb
- bace.ipynb
- dataset_Rfam_6320_13classes.fasta
- nasa.csv
- pdbbind.ipynb
- qm9.ipynb
- rna.ipynb
- tox21.ipynb
- __init__.py
- ablation_plot.py
- david.py
- time.py
- time2.py
- time_old.py
- visualize_de.py
- __init__.py
- lppdbbind
- README.md
- split.py
- train.py
- visualize.py
- __init__.py
- README.md
- split.py
- train.py
- visualize.py
- __init__.py
- README.md
- split.py
- train.py
- visualize.py
- __init__.py
- ismb_poster.py
- main_viz.py
- README.md
- utils.py
- GCA_000157115.2_Escherichia_sp_3_2_53FAA_V2_genomic.fna
- GCA_000308975.2_ASM30897v2_genomic.fna
- GCA_000597845.1_ASM59784v1_genomic.fna
- GCA_000599625.1_ASM59962v1_genomic.fna
- GCA_000599645.1_ASM59964v1_genomic.fna
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- GCA_000599685.1_ASM59968v1_genomic.fna
- GCA_000599705.1_ASM59970v1_genomic.fna
- GCF_000157115.2_Escherichia_sp_3_2_53FAA_V2_genomic.fna
- GCF_000308975.1_ASM30897v2_genomic.fna
- GCF_000597845.1_ASM59784v1_genomic.fna
- GCF_000599625.1_ASM59962v1_genomic.fna
- GCF_000599645.1_ASM59964v1_genomic.fna
- GCF_000599665.1_ASM59966v1_genomic.fna
- GCF_000599685.1_ASM59968v1_genomic.fna
- GCF_000599705.1_ASM59970v1_genomic.fna
- D001.mol
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- D001.tpl
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- 1CYN_A.pdb
- 1XO7_A.pdb
- 2HAQ_A.pdb
- 3BT8_A.pdb
- 3WOV_A.pdb
- 3ZON_A.pdb
- 4FRU_A.pdb
- 4FRV_A.pdb
- 4L00_A.pdb
- 4L01_A.pdb
- 4OLI_A.pdb
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- 4S1J_A.pdb
- 5CO1_A.pdb
- 5NX2_A.pdb
- 5TKD_A.pdb
- 5VAI_R.pdb
- 6B3J_R.pdb
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- 7AX4_A.pdb
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- 7FIM_R.pdb
- 7RTB_R.pdb
- 7S15_R.pdb
- 7X8R_R.pdb
- 8CU5_A.pdb
- drug_dist.tsv
- drug_sim.tsv
- drug_strat.tsv
- drug_weights.tsv
- drugs.h5
- drugs.pkl
- drugs.tsv
- embed.py
- inter.tsv
- prot_dist.tsv
- prot_sim.tsv
- prot_strat.tsv
- prot_weights.tsv
- seqs.fasta
- seqs.tsv
- test.csv
- train.csv
- test.csv
- train.csv
- mave_db_gold_standard_only_sequences.fasta
- mave_db_gold_standard_weights.tsv
- compounds.tsv
- mibig_compounds_data.csv
- goldstandard.protein_sequences.fasta
- weight_map_for_datasail.tsv
- RBD.fasta
- RBD_small.fasta
- ag.fasta
- CDR-H1_48_seqlen.tsv
- CDR-H1_48_seqlen_1000.tsv
- CDR-H1_seq_all.tsv
- CDR-H2_48_seqlen.tsv
- CDR-H2_48_seqlen_1000.tsv
- CDR-H2_seq_all.tsv
- CDR-H3_48_seqlen.tsv
- CDR-H3_48_seqlen_1000.tsv
- CDR-H3_seq_all.tsv
- inter.tsv
- ag.fasta
- inter.tsv
- vh.fasta
- distance_matrix.tsv
- LP_PDBBind.csv
- pdbbind_clean.fasta
- taxonomy_Phylum.tsv
- generate.py
- molecules.csv
- 1cyn_a.pdb
- 1xo7_a.pdb
- 2haq_a.pdb
- 3bt8_a.pdb
- 4fru_a.pdb
- 4frv_a.pdb
- 4s1e_a.pdb
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- 7fim_r.pdb
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- 7s15_r.pdb
- 7x8r_r.pdb
- 3wov_a.pdb
- 3zon_a.pdb
- 4l00_a.pdb
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- 4oli_a.pdb
- 5co1_a.pdb
- 5tkd_a.pdb
- 6nzr_a.pdb
- 7ax4_a.pdb
- cyclophilins.fasta
- drugs_inter.txt
- drugs_iupac.txt
- gpcrs.fasta
- kinases.fasta
- __init__.py
- pipeline_package_fixtures.py
- test_arg_validation.py
- test_basic_ilp.py
- test_bqp.py
- test_caching.py
- test_clustering.py
- test_custom_args.py
- test_leakage_eval.py
- test_overflow.py
- test_pipeline.py
- test_pipeline_package.py
- test_real_world_data.py
- test_strat.py
- test_stratification.py
- utils.py
- .gitignore
- .gitmodules
- .readthedocs.yaml
- build.sh
- CHANGELOG.md
- conftest.py
- CONTRIBUTING.md
- LICENSE
- MANIFEST.in
- meta.yaml
- pyproject.toml
- pytest.ini
- README.md
- setup.py
# Installation Guide
1. Get the code
git clone https://github.com/kalininalab/DataSAIL
Downloads the entire project code from GitHub to your computer.
cd DataSAIL
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install datasail
Installs the package published on PyPI directly β no need to clone the source.
pip install datasail numpy<2
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Python
EasyPrerequisites
pip install datasail
Installs the package published on PyPI directly β no need to clone the source.
pip install datasail numpy<2
Installs the package published on PyPI directly β no need to clone the source.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
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