├── LICENSE ├── README.md ├── image └── protFeat_banner.png ├── protFeat.toml ├── requirements.txt ├── setup.py └── src ├── input_folder └── sample.fasta ├── protFeat ├── POSSUM_Standalone_Toolkit │ ├── __init__.py │ └── src │ │ ├── __init__.py │ │ ├── featureGenerator.py │ │ ├── headerHandler.py │ │ ├── matrixTransformer.py │ │ ├── possum.py │ │ └── possum_ft.py ├── __init__.py ├── feature_extracter.py ├── iFeature │ ├── PseKRAAC │ │ ├── __init__.py │ │ ├── type1.py │ │ ├── type10.py │ │ ├── type11.py │ │ ├── type12.py │ │ ├── type13.py │ │ ├── type14.py │ │ ├── type15.py │ │ ├── type16.py │ │ ├── type2.py │ │ ├── type3A.py │ │ ├── type3B.py │ │ ├── type4.py │ │ ├── type5.py │ │ ├── type6A.py │ │ ├── type6B.py │ │ ├── type6C.py │ │ ├── type7.py │ │ ├── type8.py │ │ └── type9.py │ ├── __init__.py │ ├── cluster.py │ ├── clusters │ │ ├── __init__.py │ │ ├── apc.py │ │ ├── dbscan.py │ │ ├── hcluster.py │ │ ├── kmeans.py │ │ ├── meanshift.py │ │ ├── pca.py │ │ ├── readCode.py │ │ ├── saveCluster.py │ │ └── tsne.py │ ├── codes │ │ ├── AAC.py │ │ ├── AAINDEX.py │ │ ├── APAAC.py │ │ ├── ASA.py │ │ ├── BINARY.py │ │ ├── BLOSUM62.py │ │ ├── CKSAAGP.py │ │ ├── CKSAAP.py │ │ ├── CTDC.py │ │ ├── CTDCClass.py │ │ ├── CTDD.py │ │ ├── CTDDClass.py │ │ ├── CTDT.py │ │ ├── CTDTClass.py │ │ ├── CTriad.py │ │ ├── DDE.py │ │ ├── DPC.py │ │ ├── Disorder.py │ │ ├── DisorderB.py │ │ ├── DisorderC.py │ │ ├── EAAC.py │ │ ├── EGAAC.py │ │ ├── GAAC.py │ │ ├── GDPC.py │ │ ├── GTPC.py │ │ ├── Geary.py │ │ ├── KNNpeptide.py │ │ ├── KNNprotein.py │ │ ├── KNNprotein.v1.py │ │ ├── KSCTriad.py │ │ ├── Moran.py │ │ ├── NMBroto.py │ │ ├── NeedlemanWunsch.py │ │ ├── PAAC.py │ │ ├── PSSM.py │ │ ├── QSOrder.py │ │ ├── SOCNumber.py │ │ ├── SSEB.py │ │ ├── SSEC.py │ │ ├── TA.py │ │ ├── TPC.py │ │ ├── ZSCALE.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── AAC.cpython-37.pyc │ │ │ ├── AAC.cpython-39.pyc │ │ │ ├── AAINDEX.cpython-37.pyc │ │ │ ├── AAINDEX.cpython-39.pyc │ │ │ ├── APAAC.cpython-37.pyc │ │ │ ├── APAAC.cpython-39.pyc │ │ │ ├── ASA.cpython-37.pyc │ │ │ ├── ASA.cpython-39.pyc │ │ │ ├── BINARY.cpython-37.pyc │ │ │ ├── BINARY.cpython-39.pyc │ │ │ ├── BLOSUM62.cpython-37.pyc │ │ │ ├── BLOSUM62.cpython-39.pyc │ │ │ ├── CKSAAGP.cpython-37.pyc │ │ │ ├── CKSAAGP.cpython-39.pyc │ │ │ ├── CKSAAP.cpython-37.pyc │ │ │ ├── CKSAAP.cpython-39.pyc │ │ │ ├── CTDC.cpython-37.pyc │ │ │ ├── CTDC.cpython-39.pyc │ │ │ ├── CTDD.cpython-37.pyc │ │ │ ├── CTDD.cpython-39.pyc │ │ │ ├── CTDT.cpython-37.pyc │ │ │ ├── CTDT.cpython-39.pyc │ │ │ ├── CTriad.cpython-37.pyc │ │ │ ├── CTriad.cpython-39.pyc │ │ │ ├── DDE.cpython-37.pyc │ │ │ ├── DDE.cpython-39.pyc │ │ │ ├── DPC.cpython-37.pyc │ │ │ ├── DPC.cpython-39.pyc │ │ │ ├── Disorder.cpython-37.pyc │ │ │ ├── Disorder.cpython-39.pyc │ │ │ ├── DisorderB.cpython-37.pyc │ │ │ ├── DisorderB.cpython-39.pyc │ │ │ ├── DisorderC.cpython-37.pyc │ │ │ ├── DisorderC.cpython-39.pyc │ │ │ ├── EAAC.cpython-37.pyc │ │ │ ├── EAAC.cpython-39.pyc │ │ │ ├── EGAAC.cpython-37.pyc │ │ │ ├── EGAAC.cpython-39.pyc │ │ │ ├── GAAC.cpython-37.pyc │ │ │ ├── GAAC.cpython-39.pyc │ │ │ ├── GDPC.cpython-37.pyc │ │ │ ├── GDPC.cpython-39.pyc │ │ │ ├── GTPC.cpython-37.pyc │ │ │ ├── GTPC.cpython-39.pyc │ │ │ ├── Geary.cpython-37.pyc │ │ │ ├── Geary.cpython-39.pyc │ │ │ ├── KNNpeptide.cpython-37.pyc │ │ │ ├── KNNpeptide.cpython-39.pyc │ │ │ ├── KNNprotein.cpython-37.pyc │ │ │ ├── KNNprotein.cpython-39.pyc │ │ │ ├── KSCTriad.cpython-37.pyc │ │ │ ├── KSCTriad.cpython-39.pyc │ │ │ ├── Moran.cpython-37.pyc │ │ │ ├── Moran.cpython-39.pyc │ │ │ ├── NMBroto.cpython-37.pyc │ │ │ ├── NMBroto.cpython-39.pyc │ │ │ ├── NeedlemanWunsch.cpython-37.pyc │ │ │ ├── NeedlemanWunsch.cpython-39.pyc │ │ │ ├── PAAC.cpython-37.pyc │ │ │ ├── PAAC.cpython-39.pyc │ │ │ ├── PSSM.cpython-37.pyc │ │ │ ├── PSSM.cpython-39.pyc │ │ │ ├── QSOrder.cpython-37.pyc │ │ │ ├── QSOrder.cpython-39.pyc │ │ │ ├── SOCNumber.cpython-37.pyc │ │ │ ├── SOCNumber.cpython-39.pyc │ │ │ ├── SSEB.cpython-37.pyc │ │ │ ├── SSEB.cpython-39.pyc │ │ │ ├── SSEC.cpython-37.pyc │ │ │ ├── SSEC.cpython-39.pyc │ │ │ ├── TA.cpython-37.pyc │ │ │ ├── TA.cpython-39.pyc │ │ │ ├── TPC.cpython-37.pyc │ │ │ ├── TPC.cpython-39.pyc │ │ │ ├── ZSCALE.cpython-37.pyc │ │ │ ├── ZSCALE.cpython-39.pyc │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── checkFasta.cpython-37.pyc │ │ │ ├── checkFasta.cpython-39.pyc │ │ │ ├── readFasta.cpython-37.pyc │ │ │ ├── readFasta.cpython-39.pyc │ │ │ ├── saveCode.cpython-37.pyc │ │ │ └── saveCode.cpython-39.pyc │ │ ├── checkFasta.py │ │ ├── readFasta.py │ │ └── saveCode.py │ ├── feaSelector.py │ ├── featureSelection │ │ ├── CHI2.py │ │ ├── IG.py │ │ ├── MIC.py │ │ ├── __init__.py │ │ ├── pearsonr.py │ │ └── saveFeature.py │ ├── iFeature.py │ ├── iFeaturePseKRAAC.py │ └── scripts │ │ ├── __init__.py │ │ ├── generateDisorder.py │ │ ├── generatePSSMProfile.py │ │ ├── generateSecondaryStructure.py │ │ ├── ldaAnalysis.py │ │ ├── pcaAnalysis.py │ │ └── tsneAnalysis.py └── utils.py └── protFeat_command_line.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gozsari/ProtFeat/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gozsari/ProtFeat/HEAD/README.md -------------------------------------------------------------------------------- /image/protFeat_banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gozsari/ProtFeat/HEAD/image/protFeat_banner.png -------------------------------------------------------------------------------- /protFeat.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gozsari/ProtFeat/HEAD/protFeat.toml 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