├── .gitignore ├── LICENSE ├── README.md ├── experimental_validation ├── .gitignore ├── 1_basf_preprocessing.ipynb ├── 2a_negative_control_analysis.ipynb ├── 2b_summary_stats.ipynb ├── 2c_negative_control_analysis_higherdilution.ipynb ├── 2d_top_func_figures.ipynb ├── 3_func_signalp.ipynb ├── 3a_SignalP_seqprep.ipynb ├── 4_func_v_non_comparison.ipynb ├── 5_alignment_remote │ ├── 5c_seq_distr_swarm.ipynb │ ├── sp_msas_feb2020 │ │ ├── MGFRLKALLVGCLIFLAVSSAIA.pdf │ │ ├── MIKTLLVSSILIPCLATGA.pdf │ │ ├── MIRLKRLLAGLLLPLFVTAFG.pdf │ │ ├── MKCCRIMFVLLGLWFVFGLSVPGGRTEA.pdf │ │ ├── MKFFNPFKVIALACISGALATAQA.pdf │ │ ├── MKFLILATLSIFTGILA.pdf │ │ ├── MKFLSTAFVLLIALVAGCSTA.pdf │ │ ├── MKFQDLTLVLSLSTALA.pdf │ │ ├── MKKKIAITLLFLSLLNRA.pdf │ │ ├── MKKKIVAVLTLSVVLA.pdf │ │ ├── MKKLLILACLLISSLES.pdf │ │ ├── MKKLLVIAALACGVATAQA.pdf │ │ ├── MKKRLHIGLLLSLIAFQAGFA.pdf │ │ ├── MKKRVISALAALWLSVLGAPAVLA.pdf │ │ ├── MKKSLISFLALGLLFGSAFA.pdf │ │ ├── MKKTGFIGKTLALVIAAGMAGTAAFA.pdf │ │ ├── MKLIPNKKTLIAGILAISTSFAYS.pdf │ │ ├── MKLKKLGVILAICLGISSTFA.pdf │ │ ├── MKLLTSFVLIGALAFA.pdf │ │ ├── MKLSQSLTYLAVLGLAAGANA.pdf │ │ ├── MKMRTGKKGFLSILLAFLLVITSIPFTLVDVEA.pdf │ │ ├── MKNFATLSAVLAGATALA.pdf │ │ ├── MKVFTLAFAIICQLFASA.pdf │ │ ├── MKVFTLAFFLAIIVSQA.pdf │ │ ├── MLKKLAMAVGAMLTSISFLLPSSAQA.pdf │ │ ├── MLKRFLTLFLGFLALASSLA.pdf │ │ ├── MLKRFVKLAVIALAFAYVSA.pdf │ │ ├── MNIRLGALLAGLLLSAMASAVFA.pdf │ │ ├── MNKKFKTIMALAIATLSAAGVGVAHA.pdf │ │ ├── MQKKTAIAIAAGTAIATVAAGTQA.pdf │ │ ├── MRLIVFLATSATSLFASLA.pdf │ │ ├── MRRLFLLSSLASLSVASA.pdf │ │ ├── MSNKPAKCLAVLAAIATLSATQA.pdf │ │ ├── MTKFLLSLIFITIASALA.pdf │ │ ├── MTKLLAVIAASLMFAASTFA.pdf │ │ ├── MTRSLFIFSLLALAIFSGVSASA.pdf │ │ ├── MTSYEFLLVILGVLLSGA.pdf │ │ ├── MVSFKSALFAAAAVATVADA.pdf │ │ ├── MVSFSSLLAAASLAVVNA.pdf │ │ ├── MVSFSSLNALFLATVLA.pdf │ │ ├── MVSNKRVLALSALFGCCSLASA.pdf │ │ ├── MVTMKLRLIALAVCLCTFINASFA.pdf │ │ └── MYSLIPSLAVLAALSFAVSA.pdf │ ├── sps │ │ ├── 5a_SP_blast.ipynb │ │ ├── 5b_msa_generation.py │ │ ├── alignment_testing.ipynb │ │ ├── alns │ │ │ ├── MGFRLKALLVGCLIFLAVSSAIA.aln │ │ │ ├── MIKTLLVSSILIPCLATGA.aln │ │ │ ├── MIRLKRLLAGLLLPLFVTAFG.aln │ │ │ ├── MKCCRIMFVLLGLWFVFGLSVPGGRTEA.aln │ │ │ ├── MKFFNPFKVIALACISGALATAQA.aln │ │ │ ├── MKFLILATLSIFTGILA.aln │ │ │ ├── MKFLSTAFVLLIALVAGCSTA.aln │ │ │ ├── MKFQDLTLVLSLSTALA.aln │ │ │ ├── MKKKIAITLLFLSLLNRA.aln │ │ │ ├── MKKKIVAVLTLSVVLA.aln │ │ │ ├── MKKLLILACLLISSLES.aln │ │ │ ├── MKKLLVIAALACGVATAQA.aln │ │ │ ├── MKKRLHIGLLLSLIAFQAGFA.aln │ │ │ ├── MKKRVISALAALWLSVLGAPAVLA.aln │ │ │ ├── MKKSLISFLALGLLFGSAFA.aln │ │ │ ├── MKKTGFIGKTLALVIAAGMAGTAAFA.aln │ │ │ ├── MKLIPNKKTLIAGILAISTSFAYS.aln │ │ │ ├── MKLKKLGVILAICLGISSTFA.aln │ │ │ ├── MKLLTSFVLIGALAFA.aln │ │ │ ├── MKLSQSLTYLAVLGLAAGANA.aln │ │ │ ├── MKMRTGKKGFLSILLAFLLVITSIPFTLVDVEA.aln │ │ │ ├── MKNFATLSAVLAGATALA.aln │ │ │ ├── MKVFTLAFAIICQLFASA.aln │ │ │ ├── MKVFTLAFFLAIIVSQA.aln │ │ │ ├── MLKKLAMAVGAMLTSISFLLPSSAQA.aln │ │ │ ├── MLKRFLTLFLGFLALASSLA.aln │ │ │ ├── MLKRFVKLAVIALAFAYVSA.aln │ │ │ ├── MNIRLGALLAGLLLSAMASAVFA.aln │ │ │ ├── MNKKFKTIMALAIATLSAAGVGVAHA.aln │ │ │ ├── MQKKTAIAIAAGTAIATVAAGTQA.aln │ │ │ ├── MRLIVFLATSATSLFASLA.aln │ │ │ ├── MRRLFLLSSLASLSVASA.aln │ │ │ ├── MSNKPAKCLAVLAAIATLSATQA.aln │ │ │ ├── MTKFLLSLIFITIASALA.aln │ │ │ ├── MTKLLAVIAASLMFAASTFA.aln │ │ │ ├── MTRSLFIFSLLALAIFSGVSASA.aln │ │ │ ├── MTSYEFLLVILGVLLSGA.aln │ │ │ ├── MVSFKSALFAAAAVATVADA.aln │ │ │ ├── MVSFSSLLAAASLAVVNA.aln │ │ │ ├── MVSFSSLNALFLATVLA.aln │ │ │ ├── MVSNKRVLALSALFGCCSLASA.aln │ │ │ ├── MVTMKLRLIALAVCLCTFINASFA.aln │ │ │ ├── MYSLIPSLAVLAALSFAVSA.aln │ │ │ ├── del │ │ │ │ ├── MGFRLKALLVGCLIFLAVSSAIA.aln │ │ │ │ ├── MIKTLLVSSILIPCLATGA.aln │ │ │ │ ├── MIRLKRLLAGLLLPLFVTAFG.aln │ │ │ │ ├── MKCCRIMFVLLGLWFVFGLSVPGGRTEA.aln │ │ │ │ ├── MKFFNPFKVIALACISGALATAQA.aln │ │ │ │ ├── MKFLILATLSIFTGILA.aln │ │ │ │ ├── MKFLSTAFVLLIALVAGCSTA.aln │ │ │ │ ├── MKFQDLTLVLSLSTALA.aln │ │ │ │ ├── MKKKIAITLLFLSLLNRA.aln │ │ │ │ ├── MKKKIVAVLTLSVVLA.aln │ │ │ │ ├── MKKLLILACLLISSLES.aln │ │ │ │ ├── MKKLLVIAALACGVATAQA.aln │ │ │ │ ├── MKKRLHIGLLLSLIAFQAGFA.aln │ │ │ │ ├── MKKRVISALAALWLSVLGAPAVLA.aln │ │ │ │ ├── MKKSLISFLALGLLFGSAFA.aln │ │ │ │ ├── MKKTGFIGKTLALVIAAGMAGTAAFA.aln │ │ │ │ ├── MKLIPNKKTLIAGILAISTSFAYS.aln │ │ │ │ ├── MKLKKLGVILAICLGISSTFA.aln │ │ │ │ ├── MKLLTSFVLIGALAFA.aln │ │ │ │ ├── MKLSQSLTYLAVLGLAAGANA.aln │ │ │ │ ├── MKMRTGKKGFLSILLAFLLVITSIPFTLVDVEA.aln │ │ │ │ ├── MKNFATLSAVLAGATALA.aln │ │ │ │ ├── MKVFTLAFAIICQLFASA.aln │ │ │ │ ├── MKVFTLAFFLAIIVSQA.aln │ │ │ │ ├── MLKKLAMAVGAMLTSISFLLPSSAQA.aln │ │ │ │ ├── MLKRFLTLFLGFLALASSLA.aln │ │ │ │ ├── MLKRFVKLAVIALAFAYVSA.aln │ │ │ │ ├── MNIRLGALLAGLLLSAMASAVFA.aln │ │ │ │ ├── MNKKFKTIMALAIATLSAAGVGVAHA.aln │ │ │ │ ├── MQKKTAIAIAAGTAIATVAAGTQA.aln │ │ │ │ ├── MRLIVFLATSATSLFASLA.aln │ │ │ │ ├── MRRLFLLSSLASLSVASA.aln │ │ │ │ ├── MSNKPAKCLAVLAAIATLSATQA.aln │ │ │ │ ├── MTKFLLSLIFITIASALA.aln │ │ │ │ ├── MTKLLAVIAASLMFAASTFA.aln │ │ │ │ ├── MTRSLFIFSLLALAIFSGVSASA.aln │ │ │ │ ├── MTSYEFLLVILGVLLSGA.aln │ │ │ │ ├── MVSFKSALFAAAAVATVADA.aln │ │ │ │ ├── MVSFSSLLAAASLAVVNA.aln │ │ │ │ ├── MVSFSSLNALFLATVLA.aln │ │ │ │ ├── MVSNKRVLALSALFGCCSLASA.aln │ │ │ │ ├── MVTMKLRLIALAVCLCTFINASFA.aln │ │ │ │ ├── MYSLIPSLAVLAALSFAVSA.aln │ │ │ │ ├── func_sps_matches.csv │ │ │ │ └── func_sps_matches.xls │ │ │ └── func_sps_matches.xls │ │ ├── fasta │ │ │ ├── MGFRLKALLVGCLIFLAVSSAIA.fasta │ │ │ ├── MIKTLLVSSILIPCLATGA.fasta │ │ │ ├── MIRLKRLLAGLLLPLFVTAFG.fasta │ │ │ ├── MKCCRIMFVLLGLWFVFGLSVPGGRTEA.fasta │ │ │ ├── MKFFNPFKVIALACISGALATAQA.fasta │ │ │ ├── MKFLILATLSIFTGILA.fasta │ │ │ ├── MKFLSTAFVLLIALVAGCSTA.fasta │ │ │ ├── MKFQDLTLVLSLSTALA.fasta │ │ │ ├── MKKKIAITLLFLSLLNRA.fasta │ │ │ ├── MKKKIVAVLTLSVVLA.fasta │ │ │ ├── MKKLLILACLLISSLES.fasta │ │ │ ├── MKKLLVIAALACGVATAQA.fasta │ │ │ ├── MKKRLHIGLLLSLIAFQAGFA.fasta │ │ │ ├── MKKRVISALAALWLSVLGAPAVLA.fasta │ │ │ ├── MKKSLISFLALGLLFGSAFA.fasta │ │ │ ├── MKKTGFIGKTLALVIAAGMAGTAAFA.fasta │ │ │ ├── MKLIPNKKTLIAGILAISTSFAYS.fasta │ │ │ ├── MKLKKLGVILAICLGISSTFA.fasta │ │ │ ├── MKLLTSFVLIGALAFA.fasta │ │ │ ├── MKLSQSLTYLAVLGLAAGANA.fasta │ │ │ ├── MKMRTGKKGFLSILLAFLLVITSIPFTLVDVEA.fasta │ │ │ ├── MKNFATLSAVLAGATALA.fasta │ │ │ ├── MKVFTLAFAIICQLFASA.fasta │ │ │ ├── MKVFTLAFFLAIIVSQA.fasta │ │ │ ├── MLKKLAMAVGAMLTSISFLLPSSAQA.fasta │ │ │ ├── MLKRFLTLFLGFLALASSLA.fasta │ │ │ ├── MLKRFVKLAVIALAFAYVSA.fasta │ │ │ ├── MNIRLGALLAGLLLSAMASAVFA.fasta │ │ │ ├── MNKKFKTIMALAIATLSAAGVGVAHA.fasta │ │ │ ├── MQKKTAIAIAAGTAIATVAAGTQA.fasta │ │ │ ├── MRLIVFLATSATSLFASLA.fasta │ │ │ ├── MRRLFLLSSLASLSVASA.fasta │ │ │ ├── MSNKPAKCLAVLAAIATLSATQA.fasta │ │ │ ├── MTKFLLSLIFITIASALA.fasta │ │ │ ├── MTKLLAVIAASLMFAASTFA.fasta │ │ │ ├── MTRSLFIFSLLALAIFSGVSASA.fasta │ │ │ ├── MTSYEFLLVILGVLLSGA.fasta │ │ │ ├── MVSFKSALFAAAAVATVADA.fasta │ │ │ ├── MVSFSSLLAAASLAVVNA.fasta │ │ │ ├── MVSFSSLNALFLATVLA.fasta │ │ │ ├── MVSNKRVLALSALFGCCSLASA.fasta │ │ │ ├── MVTMKLRLIALAVCLCTFINASFA.fasta │ │ │ └── MYSLIPSLAVLAALSFAVSA.fasta │ │ ├── functional_gen_sps_200129.csv │ │ ├── sp_prot_translations.xls │ │ ├── sp_top_100_scores.csv │ │ ├── sp_top_100_scores.csv.old │ │ └── uniprot_reviewed_signalpeptides.xlsx │ └── swarm.svg ├── 6_comparisons │ ├── 6A_hmm │ │ ├── 1_hmm_prep_for_signalp.ipynb │ │ ├── all4hmmaln.fa │ │ ├── alns │ │ │ └── aln_try2_max.clustal_num │ │ ├── hmm_aligned_all.msa │ │ ├── hmm_all_out.profile │ │ ├── hmm_initial_out.profile │ │ ├── initial_gen_test.out │ │ ├── l0_4000hmm_gen_test.out │ │ ├── l0_fullhmm_gen_test.out │ │ ├── l23_4000hmm_gen_test.out │ │ ├── l23_fullhmm_gen_test.out │ │ ├── l24_4000hmm_gen_test.out │ │ ├── l24_fullhmm_gen_test.out │ │ ├── outs │ │ │ ├── l0_clustal41_signalp_input.fa │ │ │ ├── l0_clustal_gen1024.out │ │ │ ├── l0_clustal_signalp_input.fa │ │ │ ├── l0_hmm41_signalp_input.fa │ │ │ ├── l0_hmm_gen1024.out │ │ │ └── l0_hmm_signalp_input.fa │ │ ├── random_4000_foraln.txt │ │ ├── readme.txt │ │ ├── signalp_outs │ │ │ └── hmm_clustal_signalp_out.txt │ │ ├── sp2.hmm │ │ └── sp2_all_profile.sto │ ├── 6B_vae │ │ ├── 6a_vae_preprocessing.ipynb │ │ ├── 6b_vae_postprocessing.ipynb │ │ ├── 6c_VAE_LK.ipynb │ │ ├── 6d_longest_substring.ipynb │ │ ├── generated_sp_ids.xlsx │ │ ├── model_chkpts │ │ │ └── vae_e100.chkpt │ │ ├── outs │ │ │ ├── transformer_signalp_input.fa │ │ │ └── vae41_99_signalp_input.fa │ │ ├── results_1024 │ │ │ ├── sample_10.p │ │ │ ├── sample_100.p │ │ │ ├── sample_110.p │ │ │ ├── sample_120.p │ │ │ ├── sample_130.p │ │ │ ├── sample_140.p │ │ │ ├── sample_150.p │ │ │ ├── sample_160.p │ │ │ ├── sample_170.p │ │ │ ├── sample_180.p │ │ │ ├── sample_190.p │ │ │ ├── sample_20.p │ │ │ ├── sample_200.p │ │ │ ├── sample_210.p │ │ │ ├── sample_220.p │ │ │ ├── sample_230.p │ │ │ ├── sample_240.p │ │ │ ├── sample_250.p │ │ │ ├── sample_260.p │ │ │ ├── sample_270.p │ │ │ ├── sample_280.p │ │ │ ├── sample_290.p │ │ │ ├── sample_30.p │ │ │ ├── sample_300.p │ │ │ ├── sample_310.p │ │ │ ├── sample_320.p │ │ │ ├── sample_330.p │ │ │ ├── sample_340.p │ │ │ ├── sample_350.p │ │ │ ├── sample_360.p │ │ │ ├── sample_370.p │ │ │ ├── sample_380.p │ │ │ ├── sample_390.p │ │ │ ├── sample_40.p │ │ │ ├── sample_400.p │ │ │ ├── sample_410.p │ │ │ ├── sample_420.p │ │ │ ├── sample_430.p │ │ │ ├── sample_440.p │ │ │ ├── sample_450.p │ │ │ ├── sample_460.p │ │ │ ├── sample_470.p │ │ │ ├── sample_480.p │ │ │ ├── sample_490.p │ │ │ ├── sample_50.p │ │ │ ├── sample_500.p │ │ │ ├── sample_510.p │ │ │ ├── sample_520.p │ │ │ ├── sample_530.p │ │ │ ├── sample_540.p │ │ │ ├── sample_550.p │ │ │ ├── sample_560.p │ │ │ ├── sample_570.p │ │ │ ├── sample_580.p │ │ │ ├── sample_590.p │ │ │ ├── sample_60.p │ │ │ ├── sample_600.p │ │ │ ├── sample_610.p │ │ │ ├── sample_620.p │ │ │ ├── sample_630.p │ │ │ ├── sample_640.p │ │ │ ├── sample_650.p │ │ │ ├── sample_70.p │ │ │ ├── sample_80.p │ │ │ └── sample_90.p │ │ ├── training_losses99.txt │ │ ├── vae_main.py │ │ ├── vae_sp_char_dict.p │ │ ├── valid99_tensors.pt │ │ └── validate_99.pkl │ ├── 6C_comparisons │ │ ├── 6C_comparisons_to_gens.ipynb │ │ ├── comparison_plot.png │ │ ├── heuristic_plot.png │ │ ├── heuristic_signalp_out.p │ │ ├── hmm41_clustal_signalp_out.txt │ │ ├── hmm41_hmmeraln_signalp_out.txt │ │ ├── hmm_clustal_signalp_out.txt │ │ ├── hmm_hmmeraln_signalp_out.txt │ │ ├── transformer_gen_probs.p │ │ ├── vae41_99_signalp_out.txt │ │ ├── vae41_signalp_out.txt │ │ └── vae_signalp_out.txt │ └── heuristics │ │ ├── fasta_seqs.csv │ │ ├── gen_probs.p │ │ ├── heuristic.ipynb │ │ ├── heuristic_generation.txt │ │ ├── heuristic_generation_512.txt │ │ ├── heuristic_plot.png │ │ ├── initial_enzymes_1.xlsx │ │ └── signalp │ │ ├── output_protein_type-2.txt │ │ ├── output_protein_type-3.txt │ │ └── output_protein_type-4.txt ├── README.md ├── SI_Table_Generation.ipynb ├── Untitled.ipynb ├── data │ ├── 191203_combined_data.csv │ ├── 191203_mastersheet_BGsubtracted_raw.xls │ ├── SI_Table_4_merged_enzyme_info.xlsx │ ├── final_plot_ids_2.p │ ├── initial_enzymes_1.xlsx │ ├── prot_sps_bs5.txt │ ├── signalp_stats │ │ └── output_protein_type_appendedga.txt │ ├── sp_prot_translations.xls │ └── tidy_processed_sps.csv └── validation_env.yml └── remote_generation ├── README.md ├── attention-is-all-you-need-pytorch ├── .gitignore ├── DataLoader.py ├── LICENSE ├── README.md ├── preprocess.py ├── setup.py ├── train.py ├── transformer │ ├── Beam.py │ ├── Constants.py │ ├── Layers.py │ ├── Models.py │ ├── Modules.py │ ├── Optim.py │ ├── SubLayers.py │ ├── Translator.py │ └── __init__.py └── translate.py ├── signal_peptide ├── code │ ├── .ipynb_checkpoints │ │ ├── 1_initial_analysis-checkpoint.ipynb │ │ ├── 2a_one_hot_75_6-14-18_filtered-checkpoint.ipynb │ │ ├── 2b_one_hot_90_6-14-18_filtered-checkpoint.ipynb │ │ ├── 2c_one_hot_95_6-14-18_filtered-checkpoint.ipynb │ │ ├── 2d_one_hot_99_6-14-18_filtered-checkpoint.ipynb │ │ ├── 3_pytorch_pairs_training-checkpoint.ipynb │ │ ├── 4_testgeneration-Copy1-checkpoint.ipynb │ │ ├── 4_testgeneration-checkpoint.ipynb │ │ ├── Untitled-checkpoint.ipynb │ │ ├── del_2_one_hot-checkpoint.ipynb │ │ ├── one_hot-checkpoint.ipynb │ │ ├── one_hot-test_batch-Copy1-checkpoint.ipynb │ │ ├── one_hot-test_batch-checkpoint.ipynb │ │ ├── pytorch_pairs (for loop hyperpar)-checkpoint.ipynb │ │ ├── pytorch_pairs-AXA-checkpoint.ipynb │ │ ├── pytorch_pairs-AXA2-checkpoint.ipynb │ │ ├── pytorch_pairs-simplified-checkpoint.ipynb │ │ ├── seq2seq_experiments-checkpoint.ipynb │ │ ├── splits_test_batch-checkpoint.ipynb │ │ ├── splits_with_species-exp_seqanal_UPDATED-filtered_datasets_notest-checkpoint.ipynb │ │ └── translator-checkpoint.py │ ├── 1a_analysis.ipynb │ ├── 1b_splits.ipynb │ ├── 2a_one_hot_75_6-14-18_filtered.ipynb │ ├── 2b_one_hot_90_6-14-18_filtered.ipynb │ ├── 2c_one_hot_95_6-14-18_filtered.ipynb │ ├── 2d_one_hot_99_6-14-18_filtered.ipynb │ ├── 3_pytorch_pairs_training.ipynb │ ├── 4_testgeneration.ipynb │ ├── 4b_testgeneration_loglk.ipynb │ ├── __pycache__ │ │ ├── tools.cpython-36.pyc │ │ └── translator.cpython-36.pyc │ ├── tools.py │ └── 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