.gitignore
LICENSE
README.md
predict.py
predict_genome.py
setup.py
summary.png
train.py
DeepSecE/__init__.py
DeepSecE/dataset.py
DeepSecE/model.py
DeepSecE/module.py
DeepSecE/trainer.py
DeepSecE/utils.py
DeepSecE.egg-info/PKG-INFO
DeepSecE.egg-info/SOURCES.txt
DeepSecE.egg-info/dependency_links.txt
DeepSecE.egg-info/requires.txt
DeepSecE.egg-info/top_level.txt
data/Test-260.fasta
data/Train-2918.fasta
data/TXSS/definitions/CONJ.xml
data/TXSS/definitions/Flagellum.xml
data/TXSS/definitions/T1SS.xml
data/TXSS/definitions/T2SS.xml
data/TXSS/definitions/T3SS.xml
data/TXSS/definitions/T4P.xml
data/TXSS/definitions/T4SS_typeB.xml
data/TXSS/definitions/T4SS_typeC.xml
data/TXSS/definitions/T4SS_typeF.xml
data/TXSS/definitions/T4SS_typeG.xml
data/TXSS/definitions/T4SS_typeI.xml
data/TXSS/definitions/T4SS_typeT.xml
data/TXSS/definitions/T5aSS.xml
data/TXSS/definitions/T5bSS.xml
data/TXSS/definitions/T5cSS.xml
data/TXSS/definitions/T6SSi.xml
data/TXSS/definitions/T6SSii.xml
data/TXSS/definitions/T6SSiii.xml
data/TXSS/definitions/T9SS.xml
data/TXSS/definitions/Tad.xml
data/TXSS/definitions/pT4SSi.xml
data/TXSS/definitions/pT4SSt.xml
data/TXSS/profiles/Flg_flgB.hmm
data/TXSS/profiles/Flg_flgC.hmm
data/TXSS/profiles/Flg_fliE.hmm
data/TXSS/profiles/Flg_sctJ_FLG.hmm
data/TXSS/profiles/Flg_sctN_FLG.hmm
data/TXSS/profiles/Flg_sctQ_FLG.hmm
data/TXSS/profiles/Flg_sctR_FLG.hmm
data/TXSS/profiles/Flg_sctS_FLG.hmm
data/TXSS/profiles/Flg_sctT_FLG.hmm
data/TXSS/profiles/Flg_sctU_FLG.hmm
data/TXSS/profiles/Flg_sctV_FLG.hmm
data/TXSS/profiles/T1SS_abc.hmm
data/TXSS/profiles/T1SS_mfp.hmm
data/TXSS/profiles/T1SS_omf.hmm
data/TXSS/profiles/T2SS_gspC.hmm
data/TXSS/profiles/T2SS_gspD.hmm
data/TXSS/profiles/T2SS_gspE.hmm
data/TXSS/profiles/T2SS_gspF.hmm
data/TXSS/profiles/T2SS_gspG.hmm
data/TXSS/profiles/T2SS_gspH.hmm
data/TXSS/profiles/T2SS_gspI.hmm
data/TXSS/profiles/T2SS_gspJ.hmm
data/TXSS/profiles/T2SS_gspK.hmm
data/TXSS/profiles/T2SS_gspL.hmm
data/TXSS/profiles/T2SS_gspM.hmm
data/TXSS/profiles/T2SS_gspN.hmm
data/TXSS/profiles/T2SS_gspO.hmm
data/TXSS/profiles/T3SS_sctC.hmm
data/TXSS/profiles/T3SS_sctJ.hmm
data/TXSS/profiles/T3SS_sctN.hmm
data/TXSS/profiles/T3SS_sctQ.hmm
data/TXSS/profiles/T3SS_sctR.hmm
data/TXSS/profiles/T3SS_sctS.hmm
data/TXSS/profiles/T3SS_sctT.hmm
data/TXSS/profiles/T3SS_sctU.hmm
data/TXSS/profiles/T3SS_sctV.hmm
data/TXSS/profiles/T4P_pilAE.hmm
data/TXSS/profiles/T4P_pilB.hmm
data/TXSS/profiles/T4P_pilC.hmm
data/TXSS/profiles/T4P_pilD.hmm
data/TXSS/profiles/T4P_pilI_pilV.hmm
data/TXSS/profiles/T4P_pilM.hmm
data/TXSS/profiles/T4P_pilN.hmm
data/TXSS/profiles/T4P_pilO.hmm
data/TXSS/profiles/T4P_pilP.hmm
data/TXSS/profiles/T4P_pilQ.hmm
data/TXSS/profiles/T4P_pilT_pilU.hmm
data/TXSS/profiles/T4SS_B_traE.hmm
data/TXSS/profiles/T4SS_B_traF.hmm
data/TXSS/profiles/T4SS_B_traH.hmm
data/TXSS/profiles/T4SS_B_traI.hmm
data/TXSS/profiles/T4SS_B_traJ.hmm
data/TXSS/profiles/T4SS_B_traK.hmm
data/TXSS/profiles/T4SS_B_traL.hmm
data/TXSS/profiles/T4SS_B_traM.hmm
data/TXSS/profiles/T4SS_B_traN.hmm
data/TXSS/profiles/T4SS_B_traO.hmm
data/TXSS/profiles/T4SS_B_traP.hmm
data/TXSS/profiles/T4SS_B_traQ.hmm
data/TXSS/profiles/T4SS_C_alr7204.hmm
data/TXSS/profiles/T4SS_C_alr7205.hmm
data/TXSS/profiles/T4SS_C_alr7207.hmm
data/TXSS/profiles/T4SS_C_alr7208.hmm
data/TXSS/profiles/T4SS_C_alr7209.hmm
data/TXSS/profiles/T4SS_C_alr7210.hmm
data/TXSS/profiles/T4SS_C_alr7211.hmm
data/TXSS/profiles/T4SS_C_alr7212.hmm
data/TXSS/profiles/T4SS_F_traB.hmm
data/TXSS/profiles/T4SS_F_traE.hmm
data/TXSS/profiles/T4SS_F_traF.hmm
data/TXSS/profiles/T4SS_F_traG.hmm
data/TXSS/profiles/T4SS_F_traH.hmm
data/TXSS/profiles/T4SS_F_traK.hmm
data/TXSS/profiles/T4SS_F_traL.hmm
data/TXSS/profiles/T4SS_F_traN.hmm
data/TXSS/profiles/T4SS_F_traU.hmm
data/TXSS/profiles/T4SS_F_traV.hmm
data/TXSS/profiles/T4SS_F_traW.hmm
data/TXSS/profiles/T4SS_F_trbC.hmm
data/TXSS/profiles/T4SS_G_tfc10.hmm
data/TXSS/profiles/T4SS_G_tfc11.hmm
data/TXSS/profiles/T4SS_G_tfc12.hmm
data/TXSS/profiles/T4SS_G_tfc13.hmm
data/TXSS/profiles/T4SS_G_tfc14.hmm
data/TXSS/profiles/T4SS_G_tfc15.hmm
data/TXSS/profiles/T4SS_G_tfc17.hmm
data/TXSS/profiles/T4SS_G_tfc18.hmm
data/TXSS/profiles/T4SS_G_tfc19.hmm
data/TXSS/profiles/T4SS_G_tfc2.hmm
data/TXSS/profiles/T4SS_G_tfc22.hmm
data/TXSS/profiles/T4SS_G_tfc23.hmm
data/TXSS/profiles/T4SS_G_tfc24.hmm
data/TXSS/profiles/T4SS_G_tfc3.hmm
data/TXSS/profiles/T4SS_G_tfc5.hmm
data/TXSS/profiles/T4SS_G_tfc7.hmm
data/TXSS/profiles/T4SS_G_tfc8.hmm
data/TXSS/profiles/T4SS_G_tfc9.hmm
data/TXSS/profiles/T4SS_I_traE.hmm
data/TXSS/profiles/T4SS_I_traI.hmm
data/TXSS/profiles/T4SS_I_traK.hmm
data/TXSS/profiles/T4SS_I_traL.hmm
data/TXSS/profiles/T4SS_I_traM.hmm
data/TXSS/profiles/T4SS_I_traN.hmm
data/TXSS/profiles/T4SS_I_traO.hmm
data/TXSS/profiles/T4SS_I_traP.hmm
data/TXSS/profiles/T4SS_I_traQ.hmm
data/TXSS/profiles/T4SS_I_traR.hmm
data/TXSS/profiles/T4SS_I_traT.hmm
data/TXSS/profiles/T4SS_I_traU.hmm
data/TXSS/profiles/T4SS_I_traV.hmm
data/TXSS/profiles/T4SS_I_traW.hmm
data/TXSS/profiles/T4SS_I_traY.hmm
data/TXSS/profiles/T4SS_I_trbA.hmm
data/TXSS/profiles/T4SS_I_trbB.hmm
data/TXSS/profiles/T4SS_MOBB.hmm
data/TXSS/profiles/T4SS_MOBC.hmm
data/TXSS/profiles/T4SS_MOBF.hmm
data/TXSS/profiles/T4SS_MOBH.hmm
data/TXSS/profiles/T4SS_MOBP1.hmm
data/TXSS/profiles/T4SS_MOBP2.hmm
data/TXSS/profiles/T4SS_MOBP3.hmm
data/TXSS/profiles/T4SS_MOBQ.hmm
data/TXSS/profiles/T4SS_MOBT.hmm
data/TXSS/profiles/T4SS_MOBV.hmm
data/TXSS/profiles/T4SS_T_virB1.hmm
data/TXSS/profiles/T4SS_T_virB10.hmm
data/TXSS/profiles/T4SS_T_virB11.hmm
data/TXSS/profiles/T4SS_T_virB2.hmm
data/TXSS/profiles/T4SS_T_virB3.hmm
data/TXSS/profiles/T4SS_T_virB5.hmm
data/TXSS/profiles/T4SS_T_virB6.hmm
data/TXSS/profiles/T4SS_T_virB8.hmm
data/TXSS/profiles/T4SS_T_virB9.hmm
data/TXSS/profiles/T4SS_t4cp1.hmm
data/TXSS/profiles/T4SS_t4cp2.hmm
data/TXSS/profiles/T4SS_tcpA.hmm
data/TXSS/profiles/T4SS_virb4.hmm
data/TXSS/profiles/T5aSS_PF03797.hmm
data/TXSS/profiles/T5bSS_translocator.hmm
data/TXSS/profiles/T5cSS_PF03895.hmm
data/TXSS/profiles/T6SSi_evpJ.hmm
data/TXSS/profiles/T6SSi_tssA.hmm
data/TXSS/profiles/T6SSi_tssB.hmm
data/TXSS/profiles/T6SSi_tssC.hmm
data/TXSS/profiles/T6SSi_tssD.hmm
data/TXSS/profiles/T6SSi_tssE.hmm
data/TXSS/profiles/T6SSi_tssF.hmm
data/TXSS/profiles/T6SSi_tssG.hmm
data/TXSS/profiles/T6SSi_tssH.hmm
data/TXSS/profiles/T6SSi_tssI.hmm
data/TXSS/profiles/T6SSi_tssJ.hmm
data/TXSS/profiles/T6SSi_tssK.hmm
data/TXSS/profiles/T6SSi_tssL.hmm
data/TXSS/profiles/T6SSi_tssM.hmm
data/TXSS/profiles/T6SSii_dotU.hmm
data/TXSS/profiles/T6SSii_iglA.hmm
data/TXSS/profiles/T6SSii_iglB.hmm
data/TXSS/profiles/T6SSii_iglC.hmm
data/TXSS/profiles/T6SSii_iglD.hmm
data/TXSS/profiles/T6SSii_iglE.hmm
data/TXSS/profiles/T6SSii_iglF.hmm
data/TXSS/profiles/T6SSii_iglG.hmm
data/TXSS/profiles/T6SSii_iglH.hmm
data/TXSS/profiles/T6SSii_iglI.hmm
data/TXSS/profiles/T6SSii_iglJ.hmm
data/TXSS/profiles/T6SSii_pdpA.hmm
data/TXSS/profiles/T6SSii_pdpB.hmm
data/TXSS/profiles/T6SSii_pdpC.hmm
data/TXSS/profiles/T6SSii_pdpD.hmm
data/TXSS/profiles/T6SSii_pdpE.hmm
data/TXSS/profiles/T6SSii_vgrG.hmm
data/TXSS/profiles/T6SSiii_tssB.hmm
data/TXSS/profiles/T6SSiii_tssC.hmm
data/TXSS/profiles/T6SSiii_tssD.hmm
data/TXSS/profiles/T6SSiii_tssE.hmm
data/TXSS/profiles/T6SSiii_tssF.hmm
data/TXSS/profiles/T6SSiii_tssG.hmm
data/TXSS/profiles/T6SSiii_tssH.hmm
data/TXSS/profiles/T6SSiii_tssI.hmm
data/TXSS/profiles/T6SSiii_tssK.hmm
data/TXSS/profiles/T6SSiii_tssN.hmm
data/TXSS/profiles/T6SSiii_tssP.hmm
data/TXSS/profiles/T6SSiii_tssQ.hmm
data/TXSS/profiles/T9SS_gldJ_TIGR03524.hmm
data/TXSS/profiles/T9SS_gldK_TIGR03525.hmm
data/TXSS/profiles/T9SS_gldL_TIGR03513.hmm
data/TXSS/profiles/T9SS_gldM_TIGR03517.hmm
data/TXSS/profiles/T9SS_gldN_TIGR03523.hmm
data/TXSS/profiles/T9SS_porQ.hmm
data/TXSS/profiles/T9SS_porU.hmm
data/TXSS/profiles/T9SS_porV.hmm
data/TXSS/profiles/T9SS_sprA-2_PF12118.hmm
data/TXSS/profiles/T9SS_sprA-3_TIGR04189.hmm
data/TXSS/profiles/T9SS_sprA_PF14349.hmm
data/TXSS/profiles/T9SS_sprE.hmm
data/TXSS/profiles/T9SS_sprT.hmm
data/TXSS/profiles/Tad_flp.hmm
data/TXSS/profiles/Tad_rcpA.hmm
data/TXSS/profiles/Tad_tadA.hmm
data/TXSS/profiles/Tad_tadB.hmm
data/TXSS/profiles/Tad_tadC.hmm
data/TXSS/profiles/Tad_tadD.hmm
data/TXSS/profiles/Tad_tadE.hmm
data/TXSS/profiles/Tad_tadF.hmm
data/TXSS/profiles/Tad_tadV.hmm
data/TXSS/profiles/Tad_tadZ.hmm
examples/NC_002516.2_protein.fasta
examples/Test.fasta
scripts/kfold_train.sh
scripts/plot_attention.py
scripts/plot_embedding.py
scripts/plot_metrics.py