iFeature_extractor.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# https://github.com/Superzchen/iFeatureOmega-CLI\n",
    "# chrome-extension://cdonnmffkdaoajfknoeeecmchibpmkmg/assets/pdf/web/viewer.html?file=https%3A%2F%2Fraw.githubusercontent.com%2FSuperzchen%2FiFeatureOmega-CLI%2Fmain%2Fdocs%2FiFeatureOmega_manual.pdf\n",
    "import iFeatureOmegaCLI"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta copy.txt')\n",
    "pep.display_feature_types() # check all the available name\n",
    "pep.get_descriptor(\"name of feature type\")\n",
    "pep.encodings # calculate the results\n",
    "pep.to_csv('xxx_feature.csv', \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "is_executing": true
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "outputs": [],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"AAC\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"AAC.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            DPC_AA  DPC_AC  DPC_AD  DPC_AE  DPC_AF  DPC_AG  DPC_AH  DPC_AI  \\\n",
      "MDFLI          0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "MFDL           0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "MDLA           0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "LIVTQ          0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "LIVT           0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "...            ...     ...     ...     ...     ...     ...     ...     ...   \n",
      "YAEER          0.0     0.0     0.0    0.25     0.0     0.0     0.0     0.0   \n",
      "YPF            0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "YPGIA          0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "YPIL           0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "YRGGLEPINF     0.0     0.0     0.0    0.00     0.0     0.0     0.0     0.0   \n",
      "\n",
      "            DPC_AK  DPC_AL  ...  DPC_YM  DPC_YN    DPC_YP  DPC_YQ    DPC_YR  \\\n",
      "MDFLI          0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.000000   \n",
      "MFDL           0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.000000   \n",
      "MDLA           0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.000000   \n",
      "LIVTQ          0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.000000   \n",
      "LIVT           0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.000000   \n",
      "...            ...     ...  ...     ...     ...       ...     ...       ...   \n",
      "YAEER          0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.000000   \n",
      "YPF            0.0     0.0  ...     0.0     0.0  0.500000     0.0  0.000000   \n",
      "YPGIA          0.0     0.0  ...     0.0     0.0  0.250000     0.0  0.000000   \n",
      "YPIL           0.0     0.0  ...     0.0     0.0  0.333333     0.0  0.000000   \n",
      "YRGGLEPINF     0.0     0.0  ...     0.0     0.0  0.000000     0.0  0.111111   \n",
      "\n",
      "            DPC_YS  DPC_YT  DPC_YV  DPC_YW  DPC_YY  \n",
      "MDFLI          0.0     0.0     0.0     0.0     0.0  \n",
      "MFDL           0.0     0.0     0.0     0.0     0.0  \n",
      "MDLA           0.0     0.0     0.0     0.0     0.0  \n",
      "LIVTQ          0.0     0.0     0.0     0.0     0.0  \n",
      "LIVT           0.0     0.0     0.0     0.0     0.0  \n",
      "...            ...     ...     ...     ...     ...  \n",
      "YAEER          0.0     0.0     0.0     0.0     0.0  \n",
      "YPF            0.0     0.0     0.0     0.0     0.0  \n",
      "YPGIA          0.0     0.0     0.0     0.0     0.0  \n",
      "YPIL           0.0     0.0     0.0     0.0     0.0  \n",
      "YRGGLEPINF     0.0     0.0     0.0     0.0     0.0  \n",
      "\n",
      "[1020 rows x 400 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"DPC type 1\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"DPC type 1.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            TPC_AAA  TPC_AAC  TPC_AAD  TPC_AAE  TPC_AAF  TPC_AAG  TPC_AAH  \\\n",
      "MDFLI           0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "MFDL            0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "MDLA            0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "LIVTQ           0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "LIVT            0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "...             ...      ...      ...      ...      ...      ...      ...   \n",
      "YAEER           0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "YPF             0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "YPGIA           0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "YPIL            0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "YRGGLEPINF      0.0      0.0      0.0      0.0      0.0      0.0      0.0   \n",
      "\n",
      "            TPC_AAI  TPC_AAK  TPC_AAL  ...  TPC_YYM  TPC_YYN  TPC_YYP  \\\n",
      "MDFLI           0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "MFDL            0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "MDLA            0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "LIVTQ           0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "LIVT            0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "...             ...      ...      ...  ...      ...      ...      ...   \n",
      "YAEER           0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "YPF             0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "YPGIA           0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "YPIL            0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "YRGGLEPINF      0.0      0.0      0.0  ...      0.0      0.0      0.0   \n",
      "\n",
      "            TPC_YYQ  TPC_YYR  TPC_YYS  TPC_YYT  TPC_YYV  TPC_YYW  TPC_YYY  \n",
      "MDFLI           0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "MFDL            0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "MDLA            0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "LIVTQ           0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "LIVT            0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "...             ...      ...      ...      ...      ...      ...      ...  \n",
      "YAEER           0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "YPF             0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "YPGIA           0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "YPIL            0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "YRGGLEPINF      0.0      0.0      0.0      0.0      0.0      0.0      0.0  \n",
      "\n",
      "[1020 rows x 8000 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"TPC type 1\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"TPC type 1.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            CTDC_hydrophobicity_PRAM900101.G1  \\\n",
      "MDFLI                                    0.20   \n",
      "MFDL                                     0.25   \n",
      "MDLA                                     0.25   \n",
      "LIVTQ                                    0.20   \n",
      "LIVT                                     0.00   \n",
      "...                                       ...   \n",
      "YAEER                                    0.60   \n",
      "YPF                                      0.00   \n",
      "YPGIA                                    0.00   \n",
      "YPIL                                     0.00   \n",
      "YRGGLEPINF                               0.30   \n",
      "\n",
      "            CTDC_hydrophobicity_PRAM900101.G2  \\\n",
      "MDFLI                                0.000000   \n",
      "MFDL                                 0.000000   \n",
      "MDLA                                 0.250000   \n",
      "LIVTQ                                0.200000   \n",
      "LIVT                                 0.250000   \n",
      "...                                       ...   \n",
      "YAEER                                0.400000   \n",
      "YPF                                  0.666667   \n",
      "YPGIA                                0.800000   \n",
      "YPIL                                 0.500000   \n",
      "YRGGLEPINF                           0.400000   \n",
      "\n",
      "            CTDC_hydrophobicity_PRAM900101.G3  \\\n",
      "MDFLI                                0.800000   \n",
      "MFDL                                 0.750000   \n",
      "MDLA                                 0.500000   \n",
      "LIVTQ                                0.600000   \n",
      "LIVT                                 0.750000   \n",
      "...                                       ...   \n",
      "YAEER                                0.000000   \n",
      "YPF                                  0.333333   \n",
      "YPGIA                                0.200000   \n",
      "YPIL                                 0.500000   \n",
      "YRGGLEPINF                           0.300000   \n",
      "\n",
      "            CTDC_hydrophobicity_ARGP820101.G1  \\\n",
      "MDFLI                                    0.20   \n",
      "MFDL                                     0.25   \n",
      "MDLA                                     0.25   \n",
      "LIVTQ                                    0.40   \n",
      "LIVT                                     0.25   \n",
      "...                                       ...   \n",
      "YAEER                                    0.40   \n",
      "YPF                                      0.00   \n",
      "YPGIA                                    0.20   \n",
      "YPIL                                     0.00   \n",
      "YRGGLEPINF                               0.40   \n",
      "\n",
      "            CTDC_hydrophobicity_ARGP820101.G2  \\\n",
      "MDFLI                                    0.20   \n",
      "MFDL                                     0.25   \n",
      "MDLA                                     0.50   \n",
      "LIVTQ                                    0.20   \n",
      "LIVT                                     0.25   \n",
      "...                                       ...   \n",
      "YAEER                                    0.40   \n",
      "YPF                                      0.00   \n",
      "YPGIA                                    0.20   \n",
      "YPIL                                     0.00   \n",
      "YRGGLEPINF                               0.10   \n",
      "\n",
      "            CTDC_hydrophobicity_ARGP820101.G3  \\\n",
      "MDFLI                                    0.60   \n",
      "MFDL                                     0.50   \n",
      "MDLA                                     0.25   \n",
      "LIVTQ                                    0.40   \n",
      "LIVT                                     0.50   \n",
      "...                                       ...   \n",
      "YAEER                                    0.20   \n",
      "YPF                                      1.00   \n",
      "YPGIA                                    0.60   \n",
      "YPIL                                     1.00   \n",
      "YRGGLEPINF                               0.50   \n",
      "\n",
      "            CTDC_hydrophobicity_ZIMJ680101.G1  \\\n",
      "MDFLI                                    0.20   \n",
      "MFDL                                     0.25   \n",
      "MDLA                                     0.50   \n",
      "LIVTQ                                    0.40   \n",
      "LIVT                                     0.25   \n",
      "...                                       ...   \n",
      "YAEER                                    0.80   \n",
      "YPF                                      0.00   \n",
      "YPGIA                                    0.40   \n",
      "YPIL                                     0.00   \n",
      "YRGGLEPINF                               0.50   \n",
      "\n",
      "            CTDC_hydrophobicity_ZIMJ680101.G2  \\\n",
      "MDFLI                                    0.20   \n",
      "MFDL                                     0.25   \n",
      "MDLA                                     0.25   \n",
      "LIVTQ                                    0.20   \n",
      "LIVT                                     0.25   \n",
      "...                                       ...   \n",
      "YAEER                                    0.00   \n",
      "YPF                                      0.00   \n",
      "YPGIA                                    0.00   \n",
      "YPIL                                     0.00   \n",
      "YRGGLEPINF                               0.00   \n",
      "\n",
      "            CTDC_hydrophobicity_ZIMJ680101.G3  \\\n",
      "MDFLI                                    0.60   \n",
      "MFDL                                     0.50   \n",
      "MDLA                                     0.25   \n",
      "LIVTQ                                    0.40   \n",
      "LIVT                                     0.50   \n",
      "...                                       ...   \n",
      "YAEER                                    0.20   \n",
      "YPF                                      1.00   \n",
      "YPGIA                                    0.60   \n",
      "YPIL                                     1.00   \n",
      "YRGGLEPINF                               0.50   \n",
      "\n",
      "            CTDC_hydrophobicity_PONP930101.G1  ...  CTDC_polarizability.G3  \\\n",
      "MDFLI                                0.200000  ...                0.400000   \n",
      "MFDL                                 0.250000  ...                0.500000   \n",
      "MDLA                                 0.250000  ...                0.250000   \n",
      "LIVTQ                                0.400000  ...                0.000000   \n",
      "LIVT                                 0.250000  ...                0.000000   \n",
      "...                                       ...  ...                     ...   \n",
      "YAEER                                0.400000  ...                0.400000   \n",
      "YPF                                  0.333333  ...                0.666667   \n",
      "YPGIA                                0.200000  ...                0.200000   \n",
      "YPIL                                 0.250000  ...                0.250000   \n",
      "YRGGLEPINF                           0.300000  ...                0.300000   \n",
      "\n",
      "            CTDC_charge.G1  CTDC_charge.G2  CTDC_charge.G3  \\\n",
      "MDFLI                  0.0            0.80            0.20   \n",
      "MFDL                   0.0            0.75            0.25   \n",
      "MDLA                   0.0            0.75            0.25   \n",
      "LIVTQ                  0.0            1.00            0.00   \n",
      "LIVT                   0.0            1.00            0.00   \n",
      "...                    ...             ...             ...   \n",
      "YAEER                  0.2            0.40            0.40   \n",
      "YPF                    0.0            1.00            0.00   \n",
      "YPGIA                  0.0            1.00            0.00   \n",
      "YPIL                   0.0            1.00            0.00   \n",
      "YRGGLEPINF             0.1            0.80            0.10   \n",
      "\n",
      "            CTDC_secondarystruct.G1  CTDC_secondarystruct.G2  \\\n",
      "MDFLI                          0.40                 0.400000   \n",
      "MFDL                           0.50                 0.250000   \n",
      "MDLA                           0.75                 0.000000   \n",
      "LIVTQ                          0.40                 0.600000   \n",
      "LIVT                           0.25                 0.750000   \n",
      "...                             ...                      ...   \n",
      "YAEER                          0.80                 0.200000   \n",
      "YPF                            0.00                 0.666667   \n",
      "YPGIA                          0.20                 0.400000   \n",
      "YPIL                           0.25                 0.500000   \n",
      "YRGGLEPINF                     0.30                 0.300000   \n",
      "\n",
      "            CTDC_secondarystruct.G3  CTDC_solventaccess.G1  \\\n",
      "MDFLI                  2.000000e-01               0.600000   \n",
      "MFDL                   2.500000e-01               0.500000   \n",
      "MDLA                   2.500000e-01               0.500000   \n",
      "LIVTQ                  0.000000e+00               0.600000   \n",
      "LIVT                   0.000000e+00               0.750000   \n",
      "...                             ...                    ...   \n",
      "YAEER                 -5.551115e-17               0.200000   \n",
      "YPF                    3.333333e-01               0.333333   \n",
      "YPGIA                  4.000000e-01               0.600000   \n",
      "YPIL                   2.500000e-01               0.500000   \n",
      "YRGGLEPINF             4.000000e-01               0.500000   \n",
      "\n",
      "            CTDC_solventaccess.G2  CTDC_solventaccess.G3  \n",
      "MDFLI                        0.20               0.200000  \n",
      "MFDL                         0.25               0.250000  \n",
      "MDLA                         0.25               0.250000  \n",
      "LIVTQ                        0.20               0.200000  \n",
      "LIVT                         0.00               0.250000  \n",
      "...                           ...                    ...  \n",
      "YAEER                        0.60               0.200000  \n",
      "YPF                          0.00               0.666667  \n",
      "YPGIA                        0.00               0.400000  \n",
      "YPIL                         0.00               0.500000  \n",
      "YRGGLEPINF                   0.30               0.200000  \n",
      "\n",
      "[1020 rows x 39 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"CTDC\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"CTDC.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            CTDT_hydrophobicity_PRAM900101.Tr1221  \\\n",
      "MDFLI                                    0.000000   \n",
      "MFDL                                     0.000000   \n",
      "MDLA                                     0.000000   \n",
      "LIVTQ                                    0.250000   \n",
      "LIVT                                     0.000000   \n",
      "...                                           ...   \n",
      "YAEER                                    0.250000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.000000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.333333   \n",
      "\n",
      "            CTDT_hydrophobicity_PRAM900101.Tr1331  \\\n",
      "MDFLI                                    0.500000   \n",
      "MFDL                                     0.666667   \n",
      "MDLA                                     0.666667   \n",
      "LIVTQ                                    0.000000   \n",
      "LIVT                                     0.000000   \n",
      "...                                           ...   \n",
      "YAEER                                    0.000000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.000000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.333333   \n",
      "\n",
      "            CTDT_hydrophobicity_PRAM900101.Tr2332  \\\n",
      "MDFLI                                    0.000000   \n",
      "MFDL                                     0.000000   \n",
      "MDLA                                     0.333333   \n",
      "LIVTQ                                    0.250000   \n",
      "LIVT                                     0.333333   \n",
      "...                                           ...   \n",
      "YAEER                                    0.000000   \n",
      "YPF                                      0.500000   \n",
      "YPGIA                                    0.500000   \n",
      "YPIL                                     0.333333   \n",
      "YRGGLEPINF                               0.222222   \n",
      "\n",
      "            CTDT_hydrophobicity_ARGP820101.Tr1221  \\\n",
      "MDFLI                                    0.250000   \n",
      "MFDL                                     0.000000   \n",
      "MDLA                                     0.333333   \n",
      "LIVTQ                                    0.250000   \n",
      "LIVT                                     0.333333   \n",
      "...                                           ...   \n",
      "YAEER                                    0.500000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.000000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.111111   \n",
      "\n",
      "            CTDT_hydrophobicity_ARGP820101.Tr1331  \\\n",
      "MDFLI                                    0.250000   \n",
      "MFDL                                     0.666667   \n",
      "MDLA                                     0.333333   \n",
      "LIVTQ                                    0.000000   \n",
      "LIVT                                     0.000000   \n",
      "...                                           ...   \n",
      "YAEER                                    0.000000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.500000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.555556   \n",
      "\n",
      "            CTDT_hydrophobicity_ARGP820101.Tr2332  \\\n",
      "MDFLI                                    0.000000   \n",
      "MFDL                                     0.333333   \n",
      "MDLA                                     0.333333   \n",
      "LIVTQ                                    0.250000   \n",
      "LIVT                                     0.333333   \n",
      "...                                           ...   \n",
      "YAEER                                    0.250000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.250000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.111111   \n",
      "\n",
      "            CTDT_hydrophobicity_ZIMJ680101.Tr1221  \\\n",
      "MDFLI                                    0.250000   \n",
      "MFDL                                     0.000000   \n",
      "MDLA                                     0.333333   \n",
      "LIVTQ                                    0.250000   \n",
      "LIVT                                     0.333333   \n",
      "...                                           ...   \n",
      "YAEER                                    0.000000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.000000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.000000   \n",
      "\n",
      "            CTDT_hydrophobicity_ZIMJ680101.Tr1331  \\\n",
      "MDFLI                                    0.250000   \n",
      "MFDL                                     0.666667   \n",
      "MDLA                                     0.666667   \n",
      "LIVTQ                                    0.000000   \n",
      "LIVT                                     0.000000   \n",
      "...                                           ...   \n",
      "YAEER                                    0.250000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.750000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.666667   \n",
      "\n",
      "            CTDT_hydrophobicity_ZIMJ680101.Tr2332  \\\n",
      "MDFLI                                    0.000000   \n",
      "MFDL                                     0.333333   \n",
      "MDLA                                     0.000000   \n",
      "LIVTQ                                    0.250000   \n",
      "LIVT                                     0.333333   \n",
      "...                                           ...   \n",
      "YAEER                                    0.000000   \n",
      "YPF                                      0.000000   \n",
      "YPGIA                                    0.000000   \n",
      "YPIL                                     0.000000   \n",
      "YRGGLEPINF                               0.000000   \n",
      "\n",
      "            CTDT_hydrophobicity_PONP930101.Tr1221  ...  \\\n",
      "MDFLI                                        0.00  ...   \n",
      "MFDL                                         0.00  ...   \n",
      "MDLA                                         0.00  ...   \n",
      "LIVTQ                                        0.00  ...   \n",
      "LIVT                                         0.00  ...   \n",
      "...                                           ...  ...   \n",
      "YAEER                                        0.50  ...   \n",
      "YPF                                          0.00  ...   \n",
      "YPGIA                                        0.25  ...   \n",
      "YPIL                                         0.00  ...   \n",
      "YRGGLEPINF                                   0.00  ...   \n",
      "\n",
      "            CTDT_polarizability.Tr2332  CTDT_charge.Tr1221  \\\n",
      "MDFLI                         0.250000            0.000000   \n",
      "MFDL                          0.000000            0.000000   \n",
      "MDLA                          0.000000            0.000000   \n",
      "LIVTQ                         0.000000            0.000000   \n",
      "LIVT                          0.000000            0.000000   \n",
      "...                                ...                 ...   \n",
      "YAEER                         0.250000            0.000000   \n",
      "YPF                           1.000000            0.000000   \n",
      "YPGIA                         0.250000            0.000000   \n",
      "YPIL                          0.333333            0.000000   \n",
      "YRGGLEPINF                    0.111111            0.222222   \n",
      "\n",
      "            CTDT_charge.Tr1331  CTDT_charge.Tr2332  \\\n",
      "MDFLI                     0.00            0.500000   \n",
      "MFDL                      0.00            0.666667   \n",
      "MDLA                      0.00            0.666667   \n",
      "LIVTQ                     0.00            0.000000   \n",
      "LIVT                      0.00            0.000000   \n",
      "...                        ...                 ...   \n",
      "YAEER                     0.25            0.250000   \n",
      "YPF                       0.00            0.000000   \n",
      "YPGIA                     0.00            0.000000   \n",
      "YPIL                      0.00            0.000000   \n",
      "YRGGLEPINF                0.00            0.222222   \n",
      "\n",
      "            CTDT_secondarystruct.Tr1221  CTDT_secondarystruct.Tr1331  \\\n",
      "MDFLI                          0.500000                     0.250000   \n",
      "MFDL                           0.333333                     0.333333   \n",
      "MDLA                           0.000000                     0.666667   \n",
      "LIVTQ                          0.500000                     0.000000   \n",
      "LIVT                           0.333333                     0.000000   \n",
      "...                                 ...                          ...   \n",
      "YAEER                          0.250000                     0.000000   \n",
      "YPF                            0.000000                     0.000000   \n",
      "YPGIA                          0.250000                     0.000000   \n",
      "YPIL                           0.333333                     0.000000   \n",
      "YRGGLEPINF                     0.111111                     0.333333   \n",
      "\n",
      "            CTDT_secondarystruct.Tr2332  CTDT_solventaccess.Tr1221  \\\n",
      "MDFLI                          0.250000                   0.250000   \n",
      "MFDL                           0.333333                   0.666667   \n",
      "MDLA                           0.000000                   0.333333   \n",
      "LIVTQ                          0.000000                   0.000000   \n",
      "LIVT                           0.000000                   0.000000   \n",
      "...                                 ...                        ...   \n",
      "YAEER                          0.000000                   0.250000   \n",
      "YPF                            1.000000                   0.000000   \n",
      "YPGIA                          0.500000                   0.000000   \n",
      "YPIL                           0.666667                   0.000000   \n",
      "YRGGLEPINF                     0.333333                   0.444444   \n",
      "\n",
      "            CTDT_solventaccess.Tr1331  CTDT_solventaccess.Tr2332  \n",
      "MDFLI                        0.000000                   0.250000  \n",
      "MFDL                         0.333333                   0.000000  \n",
      "MDLA                         0.000000                   0.333333  \n",
      "LIVTQ                        0.250000                   0.250000  \n",
      "LIVT                         0.333333                   0.000000  \n",
      "...                               ...                        ...  \n",
      "YAEER                        0.250000                   0.000000  \n",
      "YPF                          0.500000                   0.000000  \n",
      "YPGIA                        0.250000                   0.000000  \n",
      "YPIL                         0.333333                   0.000000  \n",
      "YRGGLEPINF                   0.111111                   0.222222  \n",
      "\n",
      "[1020 rows x 39 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"CTDT\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"CTDT.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            CTDD_hydrophobicity_PRAM900101.1.residue0  \\\n",
      "MDFLI                                            40.0   \n",
      "MFDL                                             75.0   \n",
      "MDLA                                             50.0   \n",
      "LIVTQ                                           100.0   \n",
      "LIVT                                              0.0   \n",
      "...                                               ...   \n",
      "YAEER                                            60.0   \n",
      "YPF                                               0.0   \n",
      "YPGIA                                             0.0   \n",
      "YPIL                                              0.0   \n",
      "YRGGLEPINF                                       20.0   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.1.residue25  \\\n",
      "MDFLI                                             40.0   \n",
      "MFDL                                              75.0   \n",
      "MDLA                                              50.0   \n",
      "LIVTQ                                            100.0   \n",
      "LIVT                                               0.0   \n",
      "...                                                ...   \n",
      "YAEER                                             60.0   \n",
      "YPF                                                0.0   \n",
      "YPGIA                                              0.0   \n",
      "YPIL                                               0.0   \n",
      "YRGGLEPINF                                        20.0   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.1.residue50  \\\n",
      "MDFLI                                             40.0   \n",
      "MFDL                                              75.0   \n",
      "MDLA                                              50.0   \n",
      "LIVTQ                                            100.0   \n",
      "LIVT                                               0.0   \n",
      "...                                                ...   \n",
      "YAEER                                             60.0   \n",
      "YPF                                                0.0   \n",
      "YPGIA                                              0.0   \n",
      "YPIL                                               0.0   \n",
      "YRGGLEPINF                                        20.0   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.1.residue75  \\\n",
      "MDFLI                                             40.0   \n",
      "MFDL                                              75.0   \n",
      "MDLA                                              50.0   \n",
      "LIVTQ                                            100.0   \n",
      "LIVT                                               0.0   \n",
      "...                                                ...   \n",
      "YAEER                                             80.0   \n",
      "YPF                                                0.0   \n",
      "YPGIA                                              0.0   \n",
      "YPIL                                               0.0   \n",
      "YRGGLEPINF                                        60.0   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.1.residue100  \\\n",
      "MDFLI                                              40.0   \n",
      "MFDL                                               75.0   \n",
      "MDLA                                               50.0   \n",
      "LIVTQ                                             100.0   \n",
      "LIVT                                                0.0   \n",
      "...                                                 ...   \n",
      "YAEER                                             100.0   \n",
      "YPF                                                 0.0   \n",
      "YPGIA                                               0.0   \n",
      "YPIL                                                0.0   \n",
      "YRGGLEPINF                                         90.0   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.2.residue0  \\\n",
      "MDFLI                                        0.000000   \n",
      "MFDL                                         0.000000   \n",
      "MDLA                                       100.000000   \n",
      "LIVTQ                                       80.000000   \n",
      "LIVT                                       100.000000   \n",
      "...                                               ...   \n",
      "YAEER                                       20.000000   \n",
      "YPF                                         33.333333   \n",
      "YPGIA                                       20.000000   \n",
      "YPIL                                        25.000000   \n",
      "YRGGLEPINF                                  10.000000   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.2.residue25  \\\n",
      "MDFLI                                         0.000000   \n",
      "MFDL                                          0.000000   \n",
      "MDLA                                        100.000000   \n",
      "LIVTQ                                        80.000000   \n",
      "LIVT                                        100.000000   \n",
      "...                                                ...   \n",
      "YAEER                                        20.000000   \n",
      "YPF                                          33.333333   \n",
      "YPGIA                                        20.000000   \n",
      "YPIL                                         25.000000   \n",
      "YRGGLEPINF                                   10.000000   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.2.residue50  \\\n",
      "MDFLI                                         0.000000   \n",
      "MFDL                                          0.000000   \n",
      "MDLA                                        100.000000   \n",
      "LIVTQ                                        80.000000   \n",
      "LIVT                                        100.000000   \n",
      "...                                                ...   \n",
      "YAEER                                        20.000000   \n",
      "YPF                                          33.333333   \n",
      "YPGIA                                        40.000000   \n",
      "YPIL                                         25.000000   \n",
      "YRGGLEPINF                                   30.000000   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.2.residue75  \\\n",
      "MDFLI                                         0.000000   \n",
      "MFDL                                          0.000000   \n",
      "MDLA                                        100.000000   \n",
      "LIVTQ                                        80.000000   \n",
      "LIVT                                        100.000000   \n",
      "...                                                ...   \n",
      "YAEER                                        20.000000   \n",
      "YPF                                          33.333333   \n",
      "YPGIA                                        60.000000   \n",
      "YPIL                                         25.000000   \n",
      "YRGGLEPINF                                   40.000000   \n",
      "\n",
      "            CTDD_hydrophobicity_PRAM900101.2.residue100  ...  \\\n",
      "MDFLI                                          0.000000  ...   \n",
      "MFDL                                           0.000000  ...   \n",
      "MDLA                                         100.000000  ...   \n",
      "LIVTQ                                         80.000000  ...   \n",
      "LIVT                                         100.000000  ...   \n",
      "...                                                 ...  ...   \n",
      "YAEER                                         40.000000  ...   \n",
      "YPF                                           66.666667  ...   \n",
      "YPGIA                                        100.000000  ...   \n",
      "YPIL                                          50.000000  ...   \n",
      "YRGGLEPINF                                    70.000000  ...   \n",
      "\n",
      "            CTDD_solventaccess.2.residue0  CTDD_solventaccess.2.residue25  \\\n",
      "MDFLI                                40.0                            40.0   \n",
      "MFDL                                 75.0                            75.0   \n",
      "MDLA                                 50.0                            50.0   \n",
      "LIVTQ                               100.0                           100.0   \n",
      "LIVT                                  0.0                             0.0   \n",
      "...                                   ...                             ...   \n",
      "YAEER                                60.0                            60.0   \n",
      "YPF                                   0.0                             0.0   \n",
      "YPGIA                                 0.0                             0.0   \n",
      "YPIL                                  0.0                             0.0   \n",
      "YRGGLEPINF                           20.0                            20.0   \n",
      "\n",
      "            CTDD_solventaccess.2.residue50  CTDD_solventaccess.2.residue75  \\\n",
      "MDFLI                                 40.0                            40.0   \n",
      "MFDL                                  75.0                            75.0   \n",
      "MDLA                                  50.0                            50.0   \n",
      "LIVTQ                                100.0                           100.0   \n",
      "LIVT                                   0.0                             0.0   \n",
      "...                                    ...                             ...   \n",
      "YAEER                                 60.0                            80.0   \n",
      "YPF                                    0.0                             0.0   \n",
      "YPGIA                                  0.0                             0.0   \n",
      "YPIL                                   0.0                             0.0   \n",
      "YRGGLEPINF                            20.0                            60.0   \n",
      "\n",
      "            CTDD_solventaccess.2.residue100  CTDD_solventaccess.3.residue0  \\\n",
      "MDFLI                                  40.0                      20.000000   \n",
      "MFDL                                   75.0                      25.000000   \n",
      "MDLA                                   50.0                      25.000000   \n",
      "LIVTQ                                 100.0                      80.000000   \n",
      "LIVT                                    0.0                     100.000000   \n",
      "...                                     ...                            ...   \n",
      "YAEER                                 100.0                      20.000000   \n",
      "YPF                                     0.0                      33.333333   \n",
      "YPGIA                                   0.0                      20.000000   \n",
      "YPIL                                    0.0                      25.000000   \n",
      "YRGGLEPINF                             90.0                      10.000000   \n",
      "\n",
      "            CTDD_solventaccess.3.residue25  CTDD_solventaccess.3.residue50  \\\n",
      "MDFLI                            20.000000                       20.000000   \n",
      "MFDL                             25.000000                       25.000000   \n",
      "MDLA                             25.000000                       25.000000   \n",
      "LIVTQ                            80.000000                       80.000000   \n",
      "LIVT                            100.000000                      100.000000   \n",
      "...                                    ...                             ...   \n",
      "YAEER                            20.000000                       20.000000   \n",
      "YPF                              33.333333                       33.333333   \n",
      "YPGIA                            20.000000                       20.000000   \n",
      "YPIL                             25.000000                       25.000000   \n",
      "YRGGLEPINF                       10.000000                       10.000000   \n",
      "\n",
      "            CTDD_solventaccess.3.residue75  CTDD_solventaccess.3.residue100  \n",
      "MDFLI                            20.000000                        20.000000  \n",
      "MFDL                             25.000000                        25.000000  \n",
      "MDLA                             25.000000                        25.000000  \n",
      "LIVTQ                            80.000000                        80.000000  \n",
      "LIVT                            100.000000                       100.000000  \n",
      "...                                    ...                              ...  \n",
      "YAEER                            20.000000                        20.000000  \n",
      "YPF                              33.333333                        66.666667  \n",
      "YPGIA                            20.000000                        40.000000  \n",
      "YPIL                             25.000000                        50.000000  \n",
      "YRGGLEPINF                       10.000000                        70.000000  \n",
      "\n",
      "[1020 rows x 195 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"CTDD\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"CTDD.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            GAAC_alphatic  GAAC_aromatic  GAAC_postivecharge  \\\n",
      "MDFLI                0.60       0.200000                 0.0   \n",
      "MFDL                 0.50       0.250000                 0.0   \n",
      "MDLA                 0.75       0.000000                 0.0   \n",
      "LIVTQ                0.60       0.000000                 0.0   \n",
      "LIVT                 0.75       0.000000                 0.0   \n",
      "...                   ...            ...                 ...   \n",
      "YAEER                0.20       0.200000                 0.2   \n",
      "YPF                  0.00       0.666667                 0.0   \n",
      "YPGIA                0.60       0.200000                 0.0   \n",
      "YPIL                 0.50       0.250000                 0.0   \n",
      "YRGGLEPINF           0.40       0.200000                 0.1   \n",
      "\n",
      "            GAAC_negativecharge  GAAC_uncharge  \n",
      "MDFLI                      0.20       0.000000  \n",
      "MFDL                       0.25       0.000000  \n",
      "MDLA                       0.25       0.000000  \n",
      "LIVTQ                      0.00       0.400000  \n",
      "LIVT                       0.00       0.250000  \n",
      "...                         ...            ...  \n",
      "YAEER                      0.40       0.000000  \n",
      "YPF                        0.00       0.333333  \n",
      "YPGIA                      0.00       0.200000  \n",
      "YPIL                       0.00       0.250000  \n",
      "YRGGLEPINF                 0.10       0.200000  \n",
      "\n",
      "[1020 rows x 5 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"GAAC\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"GAAC.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            GDPC_alphaticr.alphaticr  GDPC_alphaticr.aromatic  \\\n",
      "MDFLI                       0.250000                 0.000000   \n",
      "MFDL                        0.000000                 0.333333   \n",
      "MDLA                        0.333333                 0.000000   \n",
      "LIVTQ                       0.500000                 0.000000   \n",
      "LIVT                        0.666667                 0.000000   \n",
      "...                              ...                      ...   \n",
      "YAEER                       0.000000                 0.000000   \n",
      "YPF                         0.000000                 0.000000   \n",
      "YPGIA                       0.500000                 0.000000   \n",
      "YPIL                        0.333333                 0.000000   \n",
      "YRGGLEPINF                  0.222222                 0.000000   \n",
      "\n",
      "            GDPC_alphaticr.postivecharger  GDPC_alphaticr.negativecharger  \\\n",
      "MDFLI                                 0.0                        0.250000   \n",
      "MFDL                                  0.0                        0.000000   \n",
      "MDLA                                  0.0                        0.333333   \n",
      "LIVTQ                                 0.0                        0.000000   \n",
      "LIVT                                  0.0                        0.000000   \n",
      "...                                   ...                             ...   \n",
      "YAEER                                 0.0                        0.250000   \n",
      "YPF                                   0.0                        0.000000   \n",
      "YPGIA                                 0.0                        0.000000   \n",
      "YPIL                                  0.0                        0.000000   \n",
      "YRGGLEPINF                            0.0                        0.111111   \n",
      "\n",
      "            GDPC_alphaticr.uncharger  GDPC_aromatic.alphaticr  \\\n",
      "MDFLI                       0.000000                     0.25   \n",
      "MFDL                        0.000000                     0.00   \n",
      "MDLA                        0.000000                     0.00   \n",
      "LIVTQ                       0.250000                     0.00   \n",
      "LIVT                        0.333333                     0.00   \n",
      "...                              ...                      ...   \n",
      "YAEER                       0.000000                     0.25   \n",
      "YPF                         0.000000                     0.00   \n",
      "YPGIA                       0.000000                     0.00   \n",
      "YPIL                        0.000000                     0.00   \n",
      "YRGGLEPINF                  0.111111                     0.00   \n",
      "\n",
      "            GDPC_aromatic.aromatic  GDPC_aromatic.postivecharger  \\\n",
      "MDFLI                          0.0                      0.000000   \n",
      "MFDL                           0.0                      0.000000   \n",
      "MDLA                           0.0                      0.000000   \n",
      "LIVTQ                          0.0                      0.000000   \n",
      "LIVT                           0.0                      0.000000   \n",
      "...                            ...                           ...   \n",
      "YAEER                          0.0                      0.000000   \n",
      "YPF                            0.0                      0.000000   \n",
      "YPGIA                          0.0                      0.000000   \n",
      "YPIL                           0.0                      0.000000   \n",
      "YRGGLEPINF                     0.0                      0.111111   \n",
      "\n",
      "            GDPC_aromatic.negativecharger  GDPC_aromatic.uncharger  ...  \\\n",
      "MDFLI                            0.000000                 0.000000  ...   \n",
      "MFDL                             0.333333                 0.000000  ...   \n",
      "MDLA                             0.000000                 0.000000  ...   \n",
      "LIVTQ                            0.000000                 0.000000  ...   \n",
      "LIVT                             0.000000                 0.000000  ...   \n",
      "...                                   ...                      ...  ...   \n",
      "YAEER                            0.000000                 0.000000  ...   \n",
      "YPF                              0.000000                 0.500000  ...   \n",
      "YPGIA                            0.000000                 0.250000  ...   \n",
      "YPIL                             0.000000                 0.333333  ...   \n",
      "YRGGLEPINF                       0.000000                 0.000000  ...   \n",
      "\n",
      "            GDPC_negativecharger.alphaticr  GDPC_negativecharger.aromatic  \\\n",
      "MDFLI                             0.000000                           0.25   \n",
      "MFDL                              0.333333                           0.00   \n",
      "MDLA                              0.333333                           0.00   \n",
      "LIVTQ                             0.000000                           0.00   \n",
      "LIVT                              0.000000                           0.00   \n",
      "...                                    ...                            ...   \n",
      "YAEER                             0.000000                           0.00   \n",
      "YPF                               0.000000                           0.00   \n",
      "YPGIA                             0.000000                           0.00   \n",
      "YPIL                              0.000000                           0.00   \n",
      "YRGGLEPINF                        0.000000                           0.00   \n",
      "\n",
      "            GDPC_negativecharger.postivecharger  \\\n",
      "MDFLI                                      0.00   \n",
      "MFDL                                       0.00   \n",
      "MDLA                                       0.00   \n",
      "LIVTQ                                      0.00   \n",
      "LIVT                                       0.00   \n",
      "...                                         ...   \n",
      "YAEER                                      0.25   \n",
      "YPF                                        0.00   \n",
      "YPGIA                                      0.00   \n",
      "YPIL                                       0.00   \n",
      "YRGGLEPINF                                 0.00   \n",
      "\n",
      "            GDPC_negativecharger.negativecharger  \\\n",
      "MDFLI                                       0.00   \n",
      "MFDL                                        0.00   \n",
      "MDLA                                        0.00   \n",
      "LIVTQ                                       0.00   \n",
      "LIVT                                        0.00   \n",
      "...                                          ...   \n",
      "YAEER                                       0.25   \n",
      "YPF                                         0.00   \n",
      "YPGIA                                       0.00   \n",
      "YPIL                                        0.00   \n",
      "YRGGLEPINF                                  0.00   \n",
      "\n",
      "            GDPC_negativecharger.uncharger  GDPC_uncharger.alphaticr  \\\n",
      "MDFLI                             0.000000                  0.000000   \n",
      "MFDL                              0.000000                  0.000000   \n",
      "MDLA                              0.000000                  0.000000   \n",
      "LIVTQ                             0.000000                  0.000000   \n",
      "LIVT                              0.000000                  0.000000   \n",
      "...                                    ...                       ...   \n",
      "YAEER                             0.000000                  0.000000   \n",
      "YPF                               0.000000                  0.000000   \n",
      "YPGIA                             0.000000                  0.250000   \n",
      "YPIL                              0.000000                  0.333333   \n",
      "YRGGLEPINF                        0.111111                  0.111111   \n",
      "\n",
      "            GDPC_uncharger.aromatic  GDPC_uncharger.postivecharger  \\\n",
      "MDFLI                      0.000000                            0.0   \n",
      "MFDL                       0.000000                            0.0   \n",
      "MDLA                       0.000000                            0.0   \n",
      "LIVTQ                      0.000000                            0.0   \n",
      "LIVT                       0.000000                            0.0   \n",
      "...                             ...                            ...   \n",
      "YAEER                      0.000000                            0.0   \n",
      "YPF                        0.500000                            0.0   \n",
      "YPGIA                      0.000000                            0.0   \n",
      "YPIL                       0.000000                            0.0   \n",
      "YRGGLEPINF                 0.111111                            0.0   \n",
      "\n",
      "            GDPC_uncharger.negativecharger  GDPC_uncharger.uncharger  \n",
      "MDFLI                                  0.0                      0.00  \n",
      "MFDL                                   0.0                      0.00  \n",
      "MDLA                                   0.0                      0.00  \n",
      "LIVTQ                                  0.0                      0.25  \n",
      "LIVT                                   0.0                      0.00  \n",
      "...                                    ...                       ...  \n",
      "YAEER                                  0.0                      0.00  \n",
      "YPF                                    0.0                      0.00  \n",
      "YPGIA                                  0.0                      0.00  \n",
      "YPIL                                   0.0                      0.00  \n",
      "YRGGLEPINF                             0.0                      0.00  \n",
      "\n",
      "[1020 rows x 25 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"GDPC type 1\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"GDPC type 1.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "            GTPC_alphaticr.alphaticr.alphaticr  \\\n",
      "MDFLI                                 0.000000   \n",
      "MFDL                                  0.000000   \n",
      "MDLA                                  0.000000   \n",
      "LIVTQ                                 0.333333   \n",
      "LIVT                                  0.500000   \n",
      "...                                        ...   \n",
      "YAEER                                 0.000000   \n",
      "YPF                                   0.000000   \n",
      "YPGIA                                 0.333333   \n",
      "YPIL                                  0.000000   \n",
      "YRGGLEPINF                            0.125000   \n",
      "\n",
      "            GTPC_alphaticr.alphaticr.aromatic  \\\n",
      "MDFLI                                     0.0   \n",
      "MFDL                                      0.0   \n",
      "MDLA                                      0.0   \n",
      "LIVTQ                                     0.0   \n",
      "LIVT                                      0.0   \n",
      "...                                       ...   \n",
      "YAEER                                     0.0   \n",
      "YPF                                       0.0   \n",
      "YPGIA                                     0.0   \n",
      "YPIL                                      0.0   \n",
      "YRGGLEPINF                                0.0   \n",
      "\n",
      "            GTPC_alphaticr.alphaticr.postivecharger  \\\n",
      "MDFLI                                           0.0   \n",
      "MFDL                                            0.0   \n",
      "MDLA                                            0.0   \n",
      "LIVTQ                                           0.0   \n",
      "LIVT                                            0.0   \n",
      "...                                             ...   \n",
      "YAEER                                           0.0   \n",
      "YPF                                             0.0   \n",
      "YPGIA                                           0.0   \n",
      "YPIL                                            0.0   \n",
      "YRGGLEPINF                                      0.0   \n",
      "\n",
      "            GTPC_alphaticr.alphaticr.negativecharger  \\\n",
      "MDFLI                                          0.000   \n",
      "MFDL                                           0.000   \n",
      "MDLA                                           0.000   \n",
      "LIVTQ                                          0.000   \n",
      "LIVT                                           0.000   \n",
      "...                                              ...   \n",
      "YAEER                                          0.000   \n",
      "YPF                                            0.000   \n",
      "YPGIA                                          0.000   \n",
      "YPIL                                           0.000   \n",
      "YRGGLEPINF                                     0.125   \n",
      "\n",
      "            GTPC_alphaticr.alphaticr.uncharger  \\\n",
      "MDFLI                                 0.000000   \n",
      "MFDL                                  0.000000   \n",
      "MDLA                                  0.000000   \n",
      "LIVTQ                                 0.333333   \n",
      "LIVT                                  0.500000   \n",
      "...                                        ...   \n",
      "YAEER                                 0.000000   \n",
      "YPF                                   0.000000   \n",
      "YPGIA                                 0.000000   \n",
      "YPIL                                  0.000000   \n",
      "YRGGLEPINF                            0.000000   \n",
      "\n",
      "            GTPC_alphaticr.aromatic.alphaticr  \\\n",
      "MDFLI                                     0.0   \n",
      "MFDL                                      0.0   \n",
      "MDLA                                      0.0   \n",
      "LIVTQ                                     0.0   \n",
      "LIVT                                      0.0   \n",
      "...                                       ...   \n",
      "YAEER                                     0.0   \n",
      "YPF                                       0.0   \n",
      "YPGIA                                     0.0   \n",
      "YPIL                                      0.0   \n",
      "YRGGLEPINF                                0.0   \n",
      "\n",
      "            GTPC_alphaticr.aromatic.aromatic  \\\n",
      "MDFLI                                    0.0   \n",
      "MFDL                                     0.0   \n",
      "MDLA                                     0.0   \n",
      "LIVTQ                                    0.0   \n",
      "LIVT                                     0.0   \n",
      "...                                      ...   \n",
      "YAEER                                    0.0   \n",
      "YPF                                      0.0   \n",
      "YPGIA                                    0.0   \n",
      "YPIL                                     0.0   \n",
      "YRGGLEPINF                               0.0   \n",
      "\n",
      "            GTPC_alphaticr.aromatic.postivecharger  \\\n",
      "MDFLI                                          0.0   \n",
      "MFDL                                           0.0   \n",
      "MDLA                                           0.0   \n",
      "LIVTQ                                          0.0   \n",
      "LIVT                                           0.0   \n",
      "...                                            ...   \n",
      "YAEER                                          0.0   \n",
      "YPF                                            0.0   \n",
      "YPGIA                                          0.0   \n",
      "YPIL                                           0.0   \n",
      "YRGGLEPINF                                     0.0   \n",
      "\n",
      "            GTPC_alphaticr.aromatic.negativecharger  \\\n",
      "MDFLI                                           0.0   \n",
      "MFDL                                            0.5   \n",
      "MDLA                                            0.0   \n",
      "LIVTQ                                           0.0   \n",
      "LIVT                                            0.0   \n",
      "...                                             ...   \n",
      "YAEER                                           0.0   \n",
      "YPF                                             0.0   \n",
      "YPGIA                                           0.0   \n",
      "YPIL                                            0.0   \n",
      "YRGGLEPINF                                      0.0   \n",
      "\n",
      "            GTPC_alphaticr.aromatic.uncharger  ...  \\\n",
      "MDFLI                                     0.0  ...   \n",
      "MFDL                                      0.0  ...   \n",
      "MDLA                                      0.0  ...   \n",
      "LIVTQ                                     0.0  ...   \n",
      "LIVT                                      0.0  ...   \n",
      "...                                       ...  ...   \n",
      "YAEER                                     0.0  ...   \n",
      "YPF                                       0.0  ...   \n",
      "YPGIA                                     0.0  ...   \n",
      "YPIL                                      0.0  ...   \n",
      "YRGGLEPINF                                0.0  ...   \n",
      "\n",
      "            GTPC_uncharger.negativecharger.alphaticr  \\\n",
      "MDFLI                                            0.0   \n",
      "MFDL                                             0.0   \n",
      "MDLA                                             0.0   \n",
      "LIVTQ                                            0.0   \n",
      "LIVT                                             0.0   \n",
      "...                                              ...   \n",
      "YAEER                                            0.0   \n",
      "YPF                                              0.0   \n",
      "YPGIA                                            0.0   \n",
      "YPIL                                             0.0   \n",
      "YRGGLEPINF                                       0.0   \n",
      "\n",
      "            GTPC_uncharger.negativecharger.aromatic  \\\n",
      "MDFLI                                           0.0   \n",
      "MFDL                                            0.0   \n",
      "MDLA                                            0.0   \n",
      "LIVTQ                                           0.0   \n",
      "LIVT                                            0.0   \n",
      "...                                             ...   \n",
      "YAEER                                           0.0   \n",
      "YPF                                             0.0   \n",
      "YPGIA                                           0.0   \n",
      "YPIL                                            0.0   \n",
      "YRGGLEPINF                                      0.0   \n",
      "\n",
      "            GTPC_uncharger.negativecharger.postivecharger  \\\n",
      "MDFLI                                                 0.0   \n",
      "MFDL                                                  0.0   \n",
      "MDLA                                                  0.0   \n",
      "LIVTQ                                                 0.0   \n",
      "LIVT                                                  0.0   \n",
      "...                                                   ...   \n",
      "YAEER                                                 0.0   \n",
      "YPF                                                   0.0   \n",
      "YPGIA                                                 0.0   \n",
      "YPIL                                                  0.0   \n",
      "YRGGLEPINF                                            0.0   \n",
      "\n",
      "            GTPC_uncharger.negativecharger.negativecharger  \\\n",
      "MDFLI                                                  0.0   \n",
      "MFDL                                                   0.0   \n",
      "MDLA                                                   0.0   \n",
      "LIVTQ                                                  0.0   \n",
      "LIVT                                                   0.0   \n",
      "...                                                    ...   \n",
      "YAEER                                                  0.0   \n",
      "YPF                                                    0.0   \n",
      "YPGIA                                                  0.0   \n",
      "YPIL                                                   0.0   \n",
      "YRGGLEPINF                                             0.0   \n",
      "\n",
      "            GTPC_uncharger.negativecharger.uncharger  \\\n",
      "MDFLI                                            0.0   \n",
      "MFDL                                             0.0   \n",
      "MDLA                                             0.0   \n",
      "LIVTQ                                            0.0   \n",
      "LIVT                                             0.0   \n",
      "...                                              ...   \n",
      "YAEER                                            0.0   \n",
      "YPF                                              0.0   \n",
      "YPGIA                                            0.0   \n",
      "YPIL                                             0.0   \n",
      "YRGGLEPINF                                       0.0   \n",
      "\n",
      "            GTPC_uncharger.uncharger.alphaticr  \\\n",
      "MDFLI                                      0.0   \n",
      "MFDL                                       0.0   \n",
      "MDLA                                       0.0   \n",
      "LIVTQ                                      0.0   \n",
      "LIVT                                       0.0   \n",
      "...                                        ...   \n",
      "YAEER                                      0.0   \n",
      "YPF                                        0.0   \n",
      "YPGIA                                      0.0   \n",
      "YPIL                                       0.0   \n",
      "YRGGLEPINF                                 0.0   \n",
      "\n",
      "            GTPC_uncharger.uncharger.aromatic  \\\n",
      "MDFLI                                     0.0   \n",
      "MFDL                                      0.0   \n",
      "MDLA                                      0.0   \n",
      "LIVTQ                                     0.0   \n",
      "LIVT                                      0.0   \n",
      "...                                       ...   \n",
      "YAEER                                     0.0   \n",
      "YPF                                       0.0   \n",
      "YPGIA                                     0.0   \n",
      "YPIL                                      0.0   \n",
      "YRGGLEPINF                                0.0   \n",
      "\n",
      "            GTPC_uncharger.uncharger.postivecharger  \\\n",
      "MDFLI                                           0.0   \n",
      "MFDL                                            0.0   \n",
      "MDLA                                            0.0   \n",
      "LIVTQ                                           0.0   \n",
      "LIVT                                            0.0   \n",
      "...                                             ...   \n",
      "YAEER                                           0.0   \n",
      "YPF                                             0.0   \n",
      "YPGIA                                           0.0   \n",
      "YPIL                                            0.0   \n",
      "YRGGLEPINF                                      0.0   \n",
      "\n",
      "            GTPC_uncharger.uncharger.negativecharger  \\\n",
      "MDFLI                                            0.0   \n",
      "MFDL                                             0.0   \n",
      "MDLA                                             0.0   \n",
      "LIVTQ                                            0.0   \n",
      "LIVT                                             0.0   \n",
      "...                                              ...   \n",
      "YAEER                                            0.0   \n",
      "YPF                                              0.0   \n",
      "YPGIA                                            0.0   \n",
      "YPIL                                             0.0   \n",
      "YRGGLEPINF                                       0.0   \n",
      "\n",
      "            GTPC_uncharger.uncharger.uncharger  \n",
      "MDFLI                                      0.0  \n",
      "MFDL                                       0.0  \n",
      "MDLA                                       0.0  \n",
      "LIVTQ                                      0.0  \n",
      "LIVT                                       0.0  \n",
      "...                                        ...  \n",
      "YAEER                                      0.0  \n",
      "YPF                                        0.0  \n",
      "YPGIA                                      0.0  \n",
      "YPIL                                       0.0  \n",
      "YRGGLEPINF                                 0.0  \n",
      "\n",
      "[1020 rows x 125 columns]\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('/Users/zhenjiaodu/Downloads')\n",
    "pep = iFeatureOmegaCLI.iProtein('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab_fasta.txt')\n",
    "# pep.display_feature_types()# check all the available name\n",
    "# pep.get_descriptor(\"name of feature type\")\n",
    "\n",
    "pep.get_descriptor(\"GTPC type 1\")\n",
    "print(pep.encodings)\n",
    "pep.to_csv(\"GTPC type 1.csv\", \"index=False\", header=False)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [
    "### extract the sequence as a singular fasta txt file, for feature extraction"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [
    "##### PseAAC"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "outputs": [],
   "source": [
    "# split the csv file into singular fasta files\n",
    "import pandas as pd\n",
    "# lodaing sequence infoeg\n",
    "seq_list_filename = 'sequence_info_after_CleanLab.csv'\n",
    "# read original y information NOTICE: must use the same sample size xlsx file for y extraction\n",
    "seq_all  = pd.read_csv(seq_list_filename, index_col=0)\n",
    "for i in range(seq_all.shape[0]):\n",
    "    seq = seq_all.iloc[i][0]\n",
    "    # print(seq)\n",
    "    seq_temp = '>'+seq+'\\n' + seq + '\\n'\n",
    "    # create a new file to write the pdb info.\n",
    "    file_name_temp = seq+'.txt'\n",
    "    f= open(file_name_temp, mode='w')\n",
    "    for line in seq_temp:\n",
    "        f.write(line)\n",
    "    f.close()"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "os.getcwd()\n",
    "os.chdir('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab')\n",
    "import glob\n",
    "# read and storage all the txt file name in working directory\n",
    "pdbqt_name = glob.glob(\"*.txt\")\n",
    "\n",
    "# pep_embeddings_collection = singular_pep\n",
    "import iFeatureOmegaCLI\n",
    "for file_name in pdbqt_name:\n",
    "    pep = iFeatureOmegaCLI.iProtein(file_name)\n",
    "    # descriptor paprameters changing\n",
    "    # /Users/zhenjiaodu/opt/anaconda3/lib/python3.8/site-packages/iFeatureOmegaCLI/parameters\n",
    "    # Protein_parameters_setting.json\n",
    "    pep.import_parameters('/Users/zhenjiaodu/opt/anaconda3/lib/python3.8/site-packages/iFeatureOmegaCLI/parameters/DProtein_parameters_setting.json')\n",
    "    pep.get_descriptor(\"PAAC\")\n",
    "    singular_pep = pep.encodings\n",
    "    # print(singular_pep)\n",
    "    pep_embeddings_collection = pd.concat([pep_embeddings_collection,singular_pep])\n",
    "    # Notice： delete the first row of the output csv, since it is duplicate with the last row"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [
    "pep_embeddings_collection = singular_pep"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "outputs": [],
   "source": [
    "pep_embeddings_collection.shape\n",
    "pep_embeddings_collection.to_csv('PseAAC_21_dimension_lambda-1,weight-0.05.csv')"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AA.txt\r\n",
      "AAATP.txt\r\n",
      "AAATPL.txt\r\n",
      "ACHP.txt\r\n",
      "ADHP.txt\r\n",
      "AEL.txt\r\n",
      "AF.txt\r\n",
      "AFKAWAVAR.txt\r\n",
      "AFKDEDTEEVPFR.txt\r\n",
      "AFL.txt\r\n",
      "AFP.txt\r\n",
      "AFVGYVLP.txt\r\n",
      "AG.txt\r\n",
      "AGLAPY.txt\r\n",
      "AGLP.txt\r\n",
      "AGP.txt\r\n",
      "AGS.txt\r\n",
      "AGSS.txt\r\n",
      "AGTTCLFTPLALPYDYSH.txt\r\n",
      "AH.txt\r\n",
      "AHEPVK.txt\r\n",
      "AHHP.txt\r\n",
      "AI.txt\r\n",
      "AIP.txt\r\n",
      "AIPP.txt\r\n",
      "AIYK.txt\r\n",
      "AKF.txt\r\n",
      "AKLEK.txt\r\n",
      "AKYCY.txt\r\n",
      "AKYSY.txt\r\n",
      "AL.txt\r\n",
      "ALAFQ.txt\r\n",
      "ALEP.txt\r\n",
      "ALNEINQFY.txt\r\n",
      "ALNEINQFYQK.txt\r\n",
      "ALPH.txt\r\n",
      "ALPHA.txt\r\n",
      "ALPM.txt\r\n",
      "ALPMHIR.txt\r\n",
      "ALPP.txt\r\n",
      "AMK.txt\r\n",
      "AMKPW.txt\r\n",
      "AMNPP.txt\r\n",
      "AMPKPW.txt\r\n",
      "AMQS.txt\r\n",
      "ANPAVVRP.txt\r\n",
      "AP.txt\r\n",
      "APER.txt\r\n",
      "APGAGVY.txt\r\n",
      "APGAPGPVG.txt\r\n",
      "APP.txt\r\n",
      "APSAK.txt\r\n",
      "APVPP.txt\r\n",
      "AQK.txt\r\n",
      "AQL.txt\r\n",
      "AQQLAAQLPAMCR.txt\r\n",
      "AQTQSLVYP.txt\r\n",
      "AR.txt\r\n",
      "ASGPINFT.txt\r\n",
      "ASL.txt\r\n",
      "ASP.txt\r\n",
      "ASYDTKF.txt\r\n",
      "ASYDTKFE.txt\r\n",
      "AV.txt\r\n",
      "AVF.txt\r\n",
      "AVPYP.txt\r\n",
      "AVPYPQR.txt\r\n",
      "AVV.txt\r\n",
      "AVVRP.txt\r\n",
      "AW.txt\r\n",
      "AWPF.txt\r\n",
      "AWW.txt\r\n",
      "AYFTPE.txt\r\n",
      "AYFYPEL.txt\r\n",
      "AYFYPELF.txt\r\n",
      "AYIASKGL.txt\r\n",
      "AYPS.txt\r\n",
      "CF.txt\r\n",
      "CFCTKPC.txt\r\n",
      "CRQNTLGHNTQTSIAQ.txt\r\n",
      "CVL.txt\r\n",
      "CVTPALR.txt\r\n",
      "CWLPVY.txt\r\n",
      "DA.txt\r\n",
      "DAGP.txt\r\n",
      "DAQSAPLRVY.txt\r\n",
      "DDTGHDFEDTGEAM.txt\r\n",
      "DELQDKIHPFAQTQSLVYPFPGPIPNS.txt\r\n",
      "DF.txt\r\n",
      "DFY.txt\r\n",
      "DGVVYY.txt\r\n",
      "DIGP.txt\r\n",
      "DIGYY.txt\r\n",
      "DILN.txt\r\n",
      "DKIHP.txt\r\n",
      "DKIHPF.txt\r\n",
      "DKVGINYW.txt\r\n",
      "DL.txt\r\n",
      "DLGP.txt\r\n",
      "DLQGK.txt\r\n",
      "DLTDY.txt\r\n",
      "DM.txt\r\n",
      "DNLLN.txt\r\n",
      "DP.txt\r\n",
      "DPYKLRP.txt\r\n",
      "DTGP.txt\r\n",
      "DTW.txt\r\n",
      "DVITGA.txt\r\n",
      "DVPPYM.txt\r\n",
      "DW.txt\r\n",
      "DYG.txt\r\n",
      "EAP.txt\r\n",
      "EAPPK.txt\r\n",
      "EDENNPFYLR.txt\r\n",
      "EEYPDL.txt\r\n",
      "EG.txt\r\n",
      "EGEPR.txt\r\n",
      "EK.txt\r\n",
      "EKERERQ.txt\r\n",
      "EKGP.txt\r\n",
      "ELIN.txt\r\n",
      "EMPFPK.txt\r\n",
      "ENGLPVHLDQSIFR.txt\r\n",
      "ENGLPVHLDQSIFRR.txt\r\n",
      "ENGLPVHLDQSIFRRP.txt\r\n",
      "ENLHLP.txt\r\n",
      "ENLHLPLP.txt\r\n",
      "ENLLRF.txt\r\n",
      "ENLLRFFVAPFPEVFG.txt\r\n",
      "EP.txt\r\n",
      "EPIPYGFLP.txt\r\n",
      "EPKAIP.txt\r\n",
      "EPR.txt\r\n",
      "EPVLGPVRGPFP.txt\r\n",
      "EQGP.txt\r\n",
      "ER.txt\r\n",
      "ERKIKVYL.txt\r\n",
      "ERYL.txt\r\n",
      "ESAGIH.txt\r\n",
      "ESI.txt\r\n",
      "ESIINF.txt\r\n",
      "EVLP.txt\r\n",
      "EVMAGNLYPG.txt\r\n",
      "FALPQY.txt\r\n",
      "FALPQYLK.txt\r\n",
      "FAQTQSLVYP.txt\r\n",
      "FC.txt\r\n",
      "FCF.txt\r\n",
      "FCVL.txt\r\n",
      "FCVLRP.txt\r\n",
      "FDART.txt\r\n",
      "FDK.txt\r\n",
      "FEDYVPLSCF.txt\r\n",
      "FEGTVFENG.txt\r\n",
      "FFGRCVSP.txt\r\n",
      "FFGVRCVSP.txt\r\n",
      "FFL.txt\r\n",
      "FFVAP.txt\r\n",
      "FFVAPFPEVFGK.txt\r\n",
      "FFYY.txt\r\n",
      "FG.txt\r\n",
      "FGASTRGA.txt\r\n",
      "FGG.txt\r\n",
      "FGK.txt\r\n",
      "FGRCVSP.txt\r\n",
      "FHERDPTHIKWGD.txt\r\n",
      "FHSGIQSEPKAIP.txt\r\n",
      "FK.txt\r\n",
      "FKGRYYP.txt\r\n",
      "FKR.txt\r\n",
      "FL.txt\r\n",
      "FNE.txt\r\n",
      "FNF.txt\r\n",
      "FNQ.txt\r\n",
      "FP.txt\r\n",
      "FPEVFGK.txt\r\n",
      "FPQYLQY.txt\r\n",
      "FQ.txt\r\n",
      "FQKVVA.txt\r\n",
      "FQKVVAG.txt\r\n",
      "FQKVVAK.txt\r\n",
      "FQPQPLIYP.txt\r\n",
      "FRADHPFL.txt\r\n",
      "FRAHPFL.txt\r\n",
      "FRC.txt\r\n",
      "FSDKIAK.txt\r\n",
      "FSY.txt\r\n",
      "FVAPFPEV.txt\r\n",
      "FVAPFPEVFG.txt\r\n",
      "FVEPIP.txt\r\n",
      "FVP.txt\r\n",
      "FVPAF.txt\r\n",
      "FW.txt\r\n",
      "FWN.txt\r\n",
      "FY.txt\r\n",
      "FYN.txt\r\n",
      "FYPEL.txt\r\n",
      "FYQQ.txt\r\n",
      "GA.txt\r\n",
      "GAAELPCSADWW.txt\r\n",
      "GAGP.txt\r\n",
      "GAPGLPGP.txt\r\n",
      "GAPGPAGPGGIPGERG.txt\r\n",
      "GAW.txt\r\n",
      "GD.txt\r\n",
      "GDLGKTTTVSNWSPPKYKDTP.txt\r\n",
      "GE.txt\r\n",
      "GEGGP.txt\r\n",
      "GEGSGA.txt\r\n",
      "GF.txt\r\n",
      "GFPGTPGLPGF.txt\r\n",
      "GFR.txt\r\n",
      "GFYPPP.txt\r\n",
      "GG.txt\r\n",
      "GGDDL.txt\r\n",
      "GGFIE.txt\r\n",
      "GGLEPI.txt\r\n",
      "GH.txt\r\n",
      "GHF.txt\r\n",
      "GHG.txt\r\n",
      "GHP.txt\r\n",
      "GHS.txt\r\n",
      "GI.txt\r\n",
      "GIL.txt\r\n",
      "GILRP.txt\r\n",
      "GIQSEPKAIP.txt\r\n",
      "GKEIIVKAER.txt\r\n",
      "GKKIATYQER.txt\r\n",
      "GKKVLQ.txt\r\n",
      "GKMVKVVSWY.txt\r\n",
      "GKP.txt\r\n",
      "GL.txt\r\n",
      "GLDIQK.txt\r\n",
      "GLG.txt\r\n",
      "GLPGSRGERGLPG.txt\r\n",
      "GLTSK.txt\r\n",
      "GLY.txt\r\n",
      "GLYP.txt\r\n",
      "GM.txt\r\n",
      "GMKCAF.txt\r\n",
      "GNGGA.txt\r\n",
      "GP.txt\r\n",
      "GPA.txt\r\n",
      "GPAGAP.txt\r\n",
      "GPAGAPGAA.txt\r\n",
      "GPCSR.txt\r\n",
      "GPFPILV.txt\r\n",
      "GPIGPA.txt\r\n",
      "GPIGPP.txt\r\n",
      "GPK.txt\r\n",
      "GPPGAIGP.txt\r\n",
      "GPPGPP.txt\r\n",
      "GPPGTDGAP.txt\r\n",
      "GPR.txt\r\n",
      "GPSMR.txt\r\n",
      "GPVGPA.txt\r\n",
      "GPVGPP.txt\r\n",
      "GQ.txt\r\n",
      "GQVPP.txt\r\n",
      "GQY.txt\r\n",
      "GR.txt\r\n",
      "GRPR.txt\r\n",
      "GS.txt\r\n",
      "GT.txt\r\n",
      "GTEKC.txt\r\n",
      "GTW.txt\r\n",
      "GV.txt\r\n",
      "GVDNPGHPF.txt\r\n",
      "GVGAGY.txt\r\n",
      "GVHHA.txt\r\n",
      "GVPKVKETMVPK.txt\r\n",
      "GVPKVKETMVPKH.txt\r\n",
      "GVQGPM.txt\r\n",
      "GVW.txt\r\n",
      "GVYPH.txt\r\n",
      "GVYPHK.txt\r\n",
      "GW.txt\r\n",
      "GY.txt\r\n",
      "GYALPHA.txt\r\n",
      "HA.txt\r\n",
      "HAEIN.txt\r\n",
      "HANENIF.txt\r\n",
      "HDHM.txt\r\n",
      "HERDPTHIKWGD.txt\r\n",
      "HFEAMR.txt\r\n",
      "HG.txt\r\n",
      "HHT.txt\r\n",
      "HHTF.txt\r\n",
      "HIK.txt\r\n",
      "HIKW.txt\r\n",
      "HIKWGD.txt\r\n",
      "HIR.txt\r\n",
      "HIRL.txt\r\n",
      "HKEMPFPKY.txt\r\n",
      "HLFGPPGKKDPV.txt\r\n",
      "HLL.txt\r\n",
      "HLPLP.txt\r\n",
      "HLPPPV.txt\r\n",
      "HNW.txt\r\n",
      "HPFAQ.txt\r\n",
      "HPFAQTQSLVYP.txt\r\n",
      "HPIKH.txt\r\n",
      "HQAAGW.txt\r\n",
      "HQDF.txt\r\n",
      "HQG.txt\r\n",
      "HQIYP.txt\r\n",
      "HSGIQSEPKAIP.txt\r\n",
      "HWTTQR.txt\r\n",
      "IA.txt\r\n",
      "IAIP.txt\r\n",
      "IAIPP.txt\r\n",
      "IAK.txt\r\n",
      "IAV.txt\r\n",
      "IAYKP.txt\r\n",
      "IAYKPAG.txt\r\n",
      "IDALNENK.txt\r\n",
      "IELPLG.txt\r\n",
      "IETWNPNNQ.txt\r\n",
      "IEW.txt\r\n",
      "IF.txt\r\n",
      "IFENLQN.txt\r\n",
      "IFL.txt\r\n",
      "IFVPA.txt\r\n",
      "IFVPAF.txt\r\n",
      "IFY.txt\r\n",
      "IG.txt\r\n",
      "IGDEPLANYL.txt\r\n",
      "IGGSI.txt\r\n",
      "IGSENSEKTTMP.txt\r\n",
      "IHPFAQTQSLVYP.txt\r\n",
      "IIAEK.txt\r\n",
      "IIP.txt\r\n",
      "IIPLEN.txt\r\n",
      "IITNW.txt\r\n",
      "IIY.txt\r\n",
      "IKP.txt\r\n",
      "IKPLDY.txt\r\n",
      "IKPLNY.txt\r\n",
      "IKPVQ.txt\r\n",
      "IKW.txt\r\n",
      "IKY.txt\r\n",
      "IL.txt\r\n",
      "ILP.txt\r\n",
      "IMY.txt\r\n",
      "INDPF.txt\r\n",
      "INSQ.txt\r\n",
      "INYWL.txt\r\n",
      "IPAIN.txt\r\n",
      "IPALLKR.txt\r\n",
      "IPAQK.txt\r\n",
      "IPAVFK.txt\r\n",
      "IPF.txt\r\n",
      "IPP.txt\r\n",
      "IPQEVLP.txt\r\n",
      "IQSEPKAIP.txt\r\n",
      "IQSQPQAFP.txt\r\n",
      "IQW.txt\r\n",
      "IR.txt\r\n",
      "IRA.txt\r\n",
      "IRAQQ.txt\r\n",
      "IRP.txt\r\n",
      "IRPV.txt\r\n",
      "IRPVQ.txt\r\n",
      "IRW.txt\r\n",
      "IRY.txt\r\n",
      "ISHIYVWK.txt\r\n",
      "ITF.txt\r\n",
      "ITMIAPSAF.txt\r\n",
      "ITT.txt\r\n",
      "ITTNP.txt\r\n",
      "IVGRPR.txt\r\n",
      "IVGRPRHQG.txt\r\n",
      "IVGRRRHQG.txt\r\n",
      "IVQ.txt\r\n",
      "IVR.txt\r\n",
      "IVRDPNGMGAW.txt\r\n",
      "IVVE.txt\r\n",
      "IVY.txt\r\n",
      "IW.txt\r\n",
      "IWH.txt\r\n",
      "IWHHT.txt\r\n",
      "IWHHTF.txt\r\n",
      "IY.txt\r\n",
      "IYLL.txt\r\n",
      "IYPR.txt\r\n",
      "IYPRY.txt\r\n",
      "IYPSFQPQPLIYP.txt\r\n",
      "KA.txt\r\n",
      "KAAAAP.txt\r\n",
      "KAAAATP.txt\r\n",
      "KAEEEYPDL.txt\r\n",
      "KAIP.txt\r\n",
      "KALPMHIRLAF.txt\r\n",
      "KAPVA.txt\r\n",
      "KDERF.txt\r\n",
      "KDQGSYEDF.txt\r\n",
      "KDVPP.txt\r\n",
      "KDYRL.txt\r\n",
      "KF.txt\r\n",
      "KFAWPQ.txt\r\n",
      "KFHSGIQSEPKAIP.txt\r\n",
      "KFY.txt\r\n",
      "KG.txt\r\n",
      "KGLWE.txt\r\n",
      "KGP.txt\r\n",
      "KGYGGVSLPEW.txt\r\n",
      "KHQDFF.txt\r\n",
      "KIEL.txt\r\n",
      "KIHPFAQAQ.txt\r\n",
      "KIHPFAQTQSLVYP.txt\r\n",
      "KIYPSFQPQPLIYP.txt\r\n",
      "KKIATYQER.txt\r\n",
      "KKPTHIKWGD.txt\r\n",
      "KLEK.txt\r\n",
      "KLKFV.txt\r\n",
      "KLP.txt\r\n",
      "KLPAGTLF.txt\r\n",
      "KLRP.txt\r\n",
      "KLSDW.txt\r\n",
      "KLYMRP.txt\r\n",
      "KP.txt\r\n",
      "KPGRP.txt\r\n",
      "KPVAAP.txt\r\n",
      "KR.txt\r\n",
      "KRQKYDI.txt\r\n",
      "KRVIQY.txt\r\n",
      "KTEIPTIN.txt\r\n",
      "KVAGPK.txt\r\n",
      "KVGTKCCAKP.txt\r\n",
      "KVHSSIQSQPQAFT.txt\r\n",
      "KVLAGM.txt\r\n",
      "KVLILA.txt\r\n",
      "KVLPG.txt\r\n",
      "KVLPVP.txt\r\n",
      "KW.txt\r\n",
      "KWL.txt\r\n",
      "KWLP.txt\r\n",
      "KY.txt\r\n",
      "KYPVQPFTESQSLTL.txt\r\n",
      "LAHKAL.txt\r\n",
      "LAIPVNKP.txt\r\n",
      "LALPP.txt\r\n",
      "LALR.txt\r\n",
      "LAMA.txt\r\n",
      "LAP.txt\r\n",
      "LAPSLPGKPKPD.txt\r\n",
      "LASPTM.txt\r\n",
      "LAY.txt\r\n",
      "LDAQSAPLR.txt\r\n",
      "LDY.txt\r\n",
      "LEE.txt\r\n",
      "LEGR.txt\r\n",
      "LEIVPK.txt\r\n",
      "LEK.txt\r\n",
      "LENLHLP.txt\r\n",
      "LENLHLPLP.txt\r\n",
      "LEPP.txt\r\n",
      "LF.txt\r\n",
      "LG.txt\r\n",
      "LGALPF.txt\r\n",
      "LGECGGR.txt\r\n",
      "LGFPTTKTYFPHF.txt\r\n",
      "LGI.txt\r\n",
      "LGV.txt\r\n",
      "LHLP.txt\r\n",
      "LHLPAP.txt\r\n",
      "LHLPGP.txt\r\n",
      "LHLPLP.txt\r\n",
      "LHLPLR.txt\r\n",
      "LHLPYP.txt\r\n",
      "LHLWLP.txt\r\n",
      "LHLYLP.txt\r\n",
      "LHP.txt\r\n",
      "LHPGDAQR.txt\r\n",
      "LIPPGVPY.txt\r\n",
      "LIVT.txt\r\n",
      "LIVTQ.txt\r\n",
      "LIWKL.txt\r\n",
      "LIY.txt\r\n",
      "LIYP.txt\r\n",
      "LK.txt\r\n",
      "LKA.txt\r\n",
      "LKIPLY.txt\r\n",
      "LKIPVA.txt\r\n",
      "LKLP.txt\r\n",
      "LKP.txt\r\n",
      "LKPMN.txt\r\n",
      "LKPNM.txt\r\n",
      "LKPTPEGN.txt\r\n",
      "LKVGVKQY.txt\r\n",
      "LKY.txt\r\n",
      "LKYPI.txt\r\n",
      "LLHSPP.txt\r\n",
      "LLLAHLL.txt\r\n",
      "LLMLDNDLPP.txt\r\n",
      "LLMPK.txt\r\n",
      "LLNP.txt\r\n",
      "LLNPPHQIYP.txt\r\n",
      "LLP.txt\r\n",
      "LLRH.txt\r\n",
      "LLYQQPVLGPVRGPFPIIV.txt\r\n",
      "LMGP.txt\r\n",
      "LNENLLRFFVAPFPEVFG.txt\r\n",
      "LNNSRAP.txt\r\n",
      "LNPA.txt\r\n",
      "LNPPHQIYP.txt\r\n",
      "LNSLT.txt\r\n",
      "LNVPGEIVE.txt\r\n",
      "LNVVGETVE.txt\r\n",
      "LPF.txt\r\n",
      "LPLP.txt\r\n",
      "LPP.txt\r\n",
      "LPPP.txt\r\n",
      "LPPPVH.txt\r\n",
      "LPYPY.txt\r\n",
      "LQP.txt\r\n",
      "LQQ.txt\r\n",
      "LQSW.txt\r\n",
      "LQW.txt\r\n",
      "LR.txt\r\n",
      "LRIPVA.txt\r\n",
      "LRP.txt\r\n",
      "LRPVAA.txt\r\n",
      "LRW.txt\r\n",
      "LRY.txt\r\n",
      "LSGNK.txt\r\n",
      "LSMGSASLSP.txt\r\n",
      "LSPA.txt\r\n",
      "LSSGDVF.txt\r\n",
      "LT.txt\r\n",
      "LTDLENLHLP.txt\r\n",
      "LTF.txt\r\n",
      "LTFPG.txt\r\n",
      "LTGP.txt\r\n",
      "LTQTPVVVPP.txt\r\n",
      "LVL.txt\r\n",
      "LVNDLVTPVFDNL.txt\r\n",
      "LVPFGW.txt\r\n",
      "LVPP.txt\r\n",
      "LVR.txt\r\n",
      "LVRT.txt\r\n",
      "LVVYPWTQ.txt\r\n",
      "LVY.txt\r\n",
      "LVYPFPGPIPNSLPQNIPP.txt\r\n",
      "LVYPFTGPIPN.txt\r\n",
      "LW.txt\r\n",
      "LY.txt\r\n",
      "LYP.txt\r\n",
      "LYPVK.txt\r\n",
      "MA.txt\r\n",
      "MAIPPKK.txt\r\n",
      "MAP.txt\r\n",
      "MAW.txt\r\n",
      "MCESASSK.txt\r\n",
      "MDFLI.txt\r\n",
      "MDLA.txt\r\n",
      "MFDL.txt\r\n",
      "MG.txt\r\n",
      "MGP.txt\r\n",
      "MIFPGAGGPEL.txt\r\n",
      "MIFPGGPQL.txt\r\n",
      "MILLLFR.txt\r\n",
      "MIPAY.txt\r\n",
      "MK.txt\r\n",
      "MKG.txt\r\n",
      "MKP.txt\r\n",
      "MKY.txt\r\n",
      "MLLCS.txt\r\n",
      "MLPAY.txt\r\n",
      "MLPVY.txt\r\n",
      "MM.txt\r\n",
      "MMVPI.txt\r\n",
      "MNP.txt\r\n",
      "MNPPK.txt\r\n",
      "MPF.txt\r\n",
      "MRW.txt\r\n",
      "MRWRD.txt\r\n",
      "MTEEY.txt\r\n",
      "MVGSAPGVL.txt\r\n",
      "MYY.txt\r\n",
      "NAGPFTPTVNREQLSTS.txt\r\n",
      "NCW.txt\r\n",
      "NENLLRFFVAPFPEVFG.txt\r\n",
      "NF.txt\r\n",
      "NG.txt\r\n",
      "NIFYCP.txt\r\n",
      "NIIPA.txt\r\n",
      "NILP.txt\r\n",
      "NIPPLTQTPV.txt\r\n",
      "NK.txt\r\n",
      "NKGPR.txt\r\n",
      "NKL.txt\r\n",
      "NKPGDML.txt\r\n",
      "NLAG.txt\r\n",
      "NLHLP.txt\r\n",
      "NLHLPLP.txt\r\n",
      "NLHLPLPLL.txt\r\n",
      "NMAINPSK.txt\r\n",
      "NNVMLQW.txt\r\n",
      "NP.txt\r\n",
      "NPP.txt\r\n",
      "NPPHQIYP.txt\r\n",
      "NSWVE.txt\r\n",
      "NVR.txt\r\n",
      "NY.txt\r\n",
      "PAAPPK.txt\r\n",
      "PADIKWGD.txt\r\n",
      "PAGPR.txt\r\n",
      "PAGPVG.txt\r\n",
      "PANIKWGD.txt\r\n",
      "PAP.txt\r\n",
      "PAPPK.txt\r\n",
      "PAQK.txt\r\n",
      "PAVVRP.txt\r\n",
      "PDLVF.txt\r\n",
      "PER.txt\r\n",
      "PFFDPQIP.txt\r\n",
      "PFP.txt\r\n",
      "PFPE.txt\r\n",
      "PFPEVFGK.txt\r\n",
      "PG.txt\r\n",
      "PGPLGLTGP.txt\r\n",
      "PGR.txt\r\n",
      "PHA.txt\r\n",
      "PHQIYP.txt\r\n",
      "PIW.txt\r\n",
      "PKAIP.txt\r\n",
      "PKHP.txt\r\n",
      "PKIDAMREKVLA.txt\r\n",
      "PKLPPVKK.txt\r\n",
      "PL.txt\r\n",
      "PLFPK.txt\r\n",
      "PLIYP.txt\r\n",
      "PLP.txt\r\n",
      "PLPLL.txt\r\n",
      "PLW.txt\r\n",
      "PNRIKYGD.txt\r\n",
      "PNSHP.txt\r\n",
      "PP.txt\r\n",
      "PPEIN.txt\r\n",
      "PPHQIYP.txt\r\n",
      "PPK.txt\r\n",
      "PPL.txt\r\n",
      "PQAFP.txt\r\n",
      "PQEVLP.txt\r\n",
      "PQNILP.txt\r\n",
      "PQPIP.txt\r\n",
      "PQPLIYP.txt\r\n",
      "PQR.txt\r\n",
      "PQTLALP.txt\r\n",
      "PRHQG.txt\r\n",
      "PRKEKLCTTS.txt\r\n",
      "PRVF.txt\r\n",
      "PRY.txt\r\n",
      "PSFQP.txt\r\n",
      "PSGQYY.txt\r\n",
      "PSNPP.txt\r\n",
      "PSSNK.txt\r\n",
      "PSY.txt\r\n",
      "PTFIAW.txt\r\n",
      "PTHIAW.txt\r\n",
      "PTHIDW.txt\r\n",
      "PTHIK.txt\r\n",
      "PTHIKW.txt\r\n",
      "PTHIKWD.txt\r\n",
      "PTHIKWG.txt\r\n",
      "PTHIKWGD.txt\r\n",
      "PTHIKWN.txt\r\n",
      "PTHVAW.txt\r\n",
      "PTPVP.txt\r\n",
      "PVGLVQPASATLYDY.txt\r\n",
      "PVNNPQIH.txt\r\n",
      "PVPP.txt\r\n",
      "PVPQP.txt\r\n",
      "PVQ.txt\r\n",
      "PYK.txt\r\n",
      "PYKLRP.txt\r\n",
      "PYKW.txt\r\n",
      "PYKWLP.txt\r\n",
      "PYP.txt\r\n",
      "PYVRYL.txt\r\n",
      "PseAAC_21_dimension_lambda-1,weight-0.05.csv\r\n",
      "QAFP.txt\r\n",
      "QAFT.txt\r\n",
      "QDNSRYTHFLTQHYDAFPQGR.txt\r\n",
      "QEVLP.txt\r\n",
      "QG.txt\r\n",
      "QGP.txt\r\n",
      "QIGLF.txt\r\n",
      "QIGP.txt\r\n",
      "QK.txt\r\n",
      "QLGFLGPR.txt\r\n",
      "QLGP.txt\r\n",
      "QLLKLK.txt\r\n",
      "QLLLQQ.txt\r\n",
      "QNALIVRYTR.txt\r\n",
      "QNILP.txt\r\n",
      "QP.txt\r\n",
      "QPIP.txt\r\n",
      "QPLIYP.txt\r\n",
      "QPQAFP.txt\r\n",
      "QPQPLIYP.txt\r\n",
      "QSEPKAIP.txt\r\n",
      "QSGP.txt\r\n",
      "QSLTL.txt\r\n",
      "QSLVYP.txt\r\n",
      "QSQPQAFP.txt\r\n",
      "QTQSLVYP.txt\r\n",
      "QVGP.txt\r\n",
      "QVPQPIP.txt\r\n",
      "QVSLNSGYY.txt\r\n",
      "QVTSTAV.txt\r\n",
      "QVVF.txt\r\n",
      "RADHP.txt\r\n",
      "RADHPF.txt\r\n",
      "RADHPFL.txt\r\n",
      "RALP.txt\r\n",
      "RDILNQ.txt\r\n",
      "RDMPIQAF.txt\r\n",
      "RELEEL.txt\r\n",
      "RELKDL.txt\r\n",
      "RF.txt\r\n",
      "RG.txt\r\n",
      "RGLSK.txt\r\n",
      "RGY.txt\r\n",
      "RHQG.txt\r\n",
      "RIGLF.txt\r\n",
      "RINK.txt\r\n",
      "RINKK.txt\r\n",
      "RIY.txt\r\n",
      "RL.txt\r\n",
      "RLPSEFDLSAFLRA.txt\r\n",
      "RLSGQTIEVTSEYLFRH.txt\r\n",
      "RML.txt\r\n",
      "RMLGQ.txt\r\n",
      "RPK.txt\r\n",
      "RPKH.txt\r\n",
      "RPKHPI.txt\r\n",
      "RPKHPIKH.txt\r\n",
      "RPKHPIKHQ.txt\r\n",
      "RPP.txt\r\n",
      "RPQIPP.txt\r\n",
      "RPR.txt\r\n",
      "RPVQ.txt\r\n",
      "RR.txt\r\n",
      "RS.txt\r\n",
      "RVPSL.txt\r\n",
      "RVR.txt\r\n",
      "RY.txt\r\n",
      "RYLG.txt\r\n",
      "RYLGY.txt\r\n",
      "SAGPM.txt\r\n",
      "SALAM.txt\r\n",
      "SAPLRVY.txt\r\n",
      "SEPKAIP.txt\r\n",
      "SF.txt\r\n",
      "SG.txt\r\n",
      "SGIQSEPKAIP.txt\r\n",
      "SGP.txt\r\n",
      "SHP.txt\r\n",
      "SIQSQPQAFP.txt\r\n",
      "SKVLPVPE.txt\r\n",
      "SKVPP.txt\r\n",
      "SKVYP.txt\r\n",
      "SKVYPFPGPI.txt\r\n",
      "SLPQ.txt\r\n",
      "SLVYP.txt\r\n",
      "SNIP.txt\r\n",
      "SPRCR.txt\r\n",
      "SPYP.txt\r\n",
      "SQPK.txt\r\n",
      "SQPQAFP.txt\r\n",
      "SSIQSQPQAFT.txt\r\n",
      "STHGVW.txt\r\n",
      "STYQT.txt\r\n",
      "SVAKL.txt\r\n",
      "SVAKLE.txt\r\n",
      "SVAKLEK.txt\r\n",
      "SVY.txt\r\n",
      "SWSF.txt\r\n",
      "SWVE.txt\r\n",
      "SY.txt\r\n",
      "TCSP.txt\r\n",
      "TD.txt\r\n",
      "TDQHQDKIYP.txt\r\n",
      "TFPHGP.txt\r\n",
      "TG.txt\r\n",
      "TGGGNV.txt\r\n",
      "TGLKP.txt\r\n",
      "TGP.txt\r\n",
      "TGPIPN.txt\r\n",
      "TGPIPNSLPQ.txt\r\n",
      "THIKWGD.txt\r\n",
      "TK.txt\r\n",
      "TKIVP.txt\r\n",
      "TKTGRSAHVLSRYRPRA.txt\r\n",
      "TKVIP.txt\r\n",
      "TKY.txt\r\n",
      "TLKYP.txt\r\n",
      "TLS.txt\r\n",
      "TNGIIR.txt\r\n",
      "TNP.txt\r\n",
      "TNW.txt\r\n",
      "TP.txt\r\n",
      "TPCPPQ.txt\r\n",
      "TPSPR.txt\r\n",
      "TPTQQS.txt\r\n",
      "TPVVVPPFLQP.txt\r\n",
      "TPWVPPFLQP.txt\r\n",
      "TQPKTNAIPY.txt\r\n",
      "TQVY.txt\r\n",
      "TTENVLFG.txt\r\n",
      "TTN.txt\r\n",
      "TVDQHQ.txt\r\n",
      "TVGMTAKF.txt\r\n",
      "TVPY.txt\r\n",
      "TVQVTSTAV.txt\r\n",
      "TVY.txt\r\n",
      "TVYTKGRVMP.txt\r\n",
      "TYCQ.txt\r\n",
      "TYLGS.txt\r\n",
      "VAA.txt\r\n",
      "VADVYVGK.txt\r\n",
      "VAE.txt\r\n",
      "VAGTW.txt\r\n",
      "VAHINVGK.txt\r\n",
      "VAHINVWK.txt\r\n",
      "VAKLEK.txt\r\n",
      "VAND.txt\r\n",
      "VAP.txt\r\n",
      "VAPFPEVF.txt\r\n",
      "VAV.txt\r\n",
      "VAW.txt\r\n",
      "VAWKL.txt\r\n",
      "VAY.txt\r\n",
      "VDF.txt\r\n",
      "VDSDVVKG.txt\r\n",
      "VECYGPNRPQF.txt\r\n",
      "VEGY.txt\r\n",
      "VELYP.txt\r\n",
      "VEV.txt\r\n",
      "VFER.txt\r\n",
      "VFKAF.txt\r\n",
      "VG.txt\r\n",
      "VGGPR.txt\r\n",
      "VGPR.txt\r\n",
      "VHLAP.txt\r\n",
      "VHLPPP.txt\r\n",
      "VHSSIQSQPQAFT.txt\r\n",
      "VHW.txt\r\n",
      "VIEKYP.txt\r\n",
      "VIGSPPEIN.txt\r\n",
      "VIIF.txt\r\n",
      "VIKP.txt\r\n",
      "VIP.txt\r\n",
      "VIPEL.txt\r\n",
      "VIY.txt\r\n",
      "VK.txt\r\n",
      "VKAGF.txt\r\n",
      "VKCFR.txt\r\n",
      "VKK.txt\r\n",
      "VKKVLGNP.txt\r\n",
      "VKP.txt\r\n",
      "VLAQYK.txt\r\n",
      "VLDTDYK.txt\r\n",
      "VLGPVRGPFPIIV.txt\r\n",
      "VLLPDEVSGL.txt\r\n",
      "VLPEI.txt\r\n",
      "VLPF.txt\r\n",
      "VLPIPQ.txt\r\n",
      "VLPYP.txt\r\n",
      "VLRP.txt\r\n",
      "VLSRYP.txt\r\n",
      "VLVPK.txt\r\n",
      "VLY.txt\r\n",
      "VM.txt\r\n",
      "VMDKPQG.txt\r\n",
      "VMP.txt\r\n",
      "VPA.txt\r\n",
      "VPFGVG.txt\r\n",
      "VPKVK.txt\r\n",
      "VPP.txt\r\n",
      "VPPAK.txt\r\n",
      "VPPLYPN.txt\r\n",
      "VPQP.txt\r\n",
      "VPQPIP.txt\r\n",
      "VPSERY.txt\r\n",
      "VPSERYL.txt\r\n",
      "VQ.txt\r\n",
      "VQV.txt\r\n",
      "VQVTSTAV.txt\r\n",
      "VR.txt\r\n",
      "VRF.txt\r\n",
      "VRGP.txt\r\n",
      "VRGPFPIIV.txt\r\n",
      "VRK.txt\r\n",
      "VRP.txt\r\n",
      "VRSP.txt\r\n",
      "VRYL.txt\r\n",
      "VSGAGRY.txt\r\n",
      "VSGP.txt\r\n",
      "VSLPEW.txt\r\n",
      "VSP.txt\r\n",
      "VSRHFASYAN.txt\r\n",
      "VSV.txt\r\n",
      "VSW.txt\r\n",
      "VTGRFAGHPAAQ.txt\r\n",
      "VTPALR.txt\r\n",
      "VTR.txt\r\n",
      "VTVNPYKWLP.txt\r\n",
      "VVCVPW.txt\r\n",
      "VVF.txt\r\n",
      "VVG.txt\r\n",
      "VVGAK.txt\r\n",
      "VVGP.txt\r\n",
      "VVPP.txt\r\n",
      "VVRP.txt\r\n",
      "VVVPP.txt\r\n",
      "VVVPPF.txt\r\n",
      "VVY.txt\r\n",
      "VVYPW.txt\r\n",
      "VVYPWT.txt\r\n",
      "VVYPWTQ.txt\r\n",
      "VVYPWTQRF.txt\r\n",
      "VW.txt\r\n",
      "VWDPPKFD.txt\r\n",
      "VWIG.txt\r\n",
      "VWIS.txt\r\n",
      "VWP.txt\r\n",
      "VWY.txt\r\n",
      "VY.txt\r\n",
      "VYAP.txt\r\n",
      "VYAPFE.txt\r\n",
      "VYNEGLPAP.txt\r\n",
      "VYPFPGPI.txt\r\n",
      "VYPHK.txt\r\n",
      "VYRT.txt\r\n",
      "WA.txt\r\n",
      "WG.txt\r\n",
      "WHHT.txt\r\n",
      "WHHTF.txt\r\n",
      "WHP.txt\r\n",
      "WIHNENQGF.txt\r\n",
      "WIR.txt\r\n",
      "WL.txt\r\n",
      "WLAHK.txt\r\n",
      "WNPR.txt\r\n",
      "WPEAAELMMEVDP.txt\r\n",
      "WPERPPQIP.txt\r\n",
      "WQVLPNAVPAK.txt\r\n",
      "WT.txt\r\n",
      "WTFR.txt\r\n",
      "WVPSV.txt\r\n",
      "WVPSVY.txt\r\n",
      "WY.txt\r\n",
      "WYSLA.txt\r\n",
      "WYSLAM.txt\r\n",
      "WYSLAMA.txt\r\n",
      "YA.txt\r\n",
      "YAEER.txt\r\n",
      "YALPHA.txt\r\n",
      "YANPAVVRP.txt\r\n",
      "YE.txt\r\n",
      "YG.txt\r\n",
      "YGFLP.txt\r\n",
      "YGG.txt\r\n",
      "YGGVSLPEW.txt\r\n",
      "YGL.txt\r\n",
      "YGLF.txt\r\n",
      "YH.txt\r\n",
      "YINQMPQKSREA.txt\r\n",
      "YK.txt\r\n",
      "YKLRP.txt\r\n",
      "YKVPQL.txt\r\n",
      "YKW.txt\r\n",
      "YKWL.txt\r\n",
      "YKWLP.txt\r\n",
      "YKY.txt\r\n",
      "YLAGNQ.txt\r\n",
      "YLGY.txt\r\n",
      "YLYEIAR.txt\r\n",
      "YN.txt\r\n",
      "YNK.txt\r\n",
      "YNKL.txt\r\n",
      "YP.txt\r\n",
      "YPER.txt\r\n",
      "YPF.txt\r\n",
      "YPFPGPIP.txt\r\n",
      "YPFPGPIPN.txt\r\n",
      "YPGIA.txt\r\n",
      "YPIL.txt\r\n",
      "YPK.txt\r\n",
      "YPLDL.txt\r\n",
      "YPLDLF.txt\r\n",
      "YPR.txt\r\n",
      "YPRY.txt\r\n",
      "YPSFQPQPLIYP.txt\r\n",
      "YQ.txt\r\n",
      "YQEP.txt\r\n",
      "YQEPVL.txt\r\n",
      "YQEPVLGP.txt\r\n",
      "YQEPVLQPVR.txt\r\n",
      "YQIGL.txt\r\n",
      "YQKFPQY.txt\r\n",
      "YQKFPQYLQY.txt\r\n",
      "YQNPRLGPTGELDPATQPIVAVHNPVIV.txt\r\n",
      "YR.txt\r\n",
      "YRGGLEPINF.txt\r\n",
      "YS.txt\r\n",
      "YSQQQQ.txt\r\n",
      "YTAGV.txt\r\n",
      "YTVF.txt\r\n",
      "YV.txt\r\n",
      "YVP.txt\r\n",
      "YVVFK.txt\r\n",
      "YW.txt\r\n",
      "YY.txt\r\n",
      "YYA.txt\r\n",
      "YYAKPAAVR.txt\r\n",
      "YYAPFE.txt\r\n",
      "YYPQIMQY.txt\r\n"
     ]
    }
   ],
   "source": [
    "singular_pep"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [
    "#### OPF_10bit              Overlapping property features - 10 bit"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "os.getcwd()\n",
    "os.chdir('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab')\n",
    "import glob\n",
    "# read and storage all the txt file name in working directory\n",
    "pdbqt_name = glob.glob(\"*.txt\")\n",
    "\n",
    "# pep_embeddings_collection = singular_pep\n",
    "import iFeatureOmegaCLI\n",
    "for file_name in pdbqt_name:\n",
    "    pep = iFeatureOmegaCLI.iProtein(file_name)\n",
    "    # descriptor paprameters changing\n",
    "    # /Users/zhenjiaodu/opt/anaconda3/lib/python3.8/site-packages/iFeatureOmegaCLI/parameters\n",
    "    # Protein_parameters_setting.json\n",
    "    pep.import_parameters('/Users/zhenjiaodu/opt/anaconda3/lib/python3.8/site-packages/iFeatureOmegaCLI/parameters/DProtein_parameters_setting.json')\n",
    "    pep.get_descriptor(\"OPF_10bit\")\n",
    "    singular_pep = pep.encodings\n",
    "    singular_extrac_N_and_C = pd.concat([singular_pep.iloc[0][0:10],singular_pep.iloc[0][-10:]],axis=0, ignore_index = True)\n",
    "    # print(singular_pep)\n",
    "    pep_embeddings_collection = pd.concat([pep_embeddings_collection,singular_extrac_N_and_C],axis=1)\n",
    "    # Notice： delete the first row of the output csv, since it is duplicate with the last row"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "outputs": [],
   "source": [
    "pep_embeddings_collection.shape\n",
    "pep_embeddings_collection.T.to_csv('OPF_10bit_NandC_only.csv')"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "outputs": [],
   "source": [
    "pep_embeddings_collection = pd.concat([pep_embeddings_collection,singular_extrac_N_and_C],axis=1)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "outputs": [],
   "source": [
    "pep_embeddings_collection = singular_extrac_N_and_C"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "outputs": [
    {
     "data": {
      "text/plain": "0     0.0\n1     0.0\n2     0.0\n3     0.0\n4     1.0\n5     1.0\n6     0.0\n7     0.0\n8     0.0\n9     0.0\n10    0.0\n11    0.0\n12    0.0\n13    0.0\n14    0.0\n15    0.0\n16    0.0\n17    0.0\n18    1.0\n19    1.0\nName: IAYKP, dtype: float64"
     },
     "execution_count": 63,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "singular_extrac_N_and_C"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "os.getcwd()\n",
    "os.chdir('/Users/zhenjiaodu/Downloads/sequence_info_after_CleanLab')\n",
    "import glob\n",
    "# read and storage all the txt file name in working directory\n",
    "pdbqt_name = glob.glob(\"*.txt\")\n",
    "\n",
    "# pep_embeddings_collection = singular_pep\n",
    "import iFeatureOmegaCLI\n",
    "for file_name in pdbqt_name:\n",
    "    pep = iFeatureOmegaCLI.iProtein(file_name)\n",
    "    # descriptor paprameters changing\n",
    "    # /Users/zhenjiaodu/opt/anaconda3/lib/python3.8/site-packages/iFeatureOmegaCLI/parameters\n",
    "    # Protein_parameters_setting.json\n",
    "    pep.import_parameters('/Users/zhenjiaodu/opt/anaconda3/lib/python3.8/site-packages/iFeatureOmegaCLI/parameters/DProtein_parameters_setting.json')\n",
    "    pep.get_descriptor(\"AAIndex\")\n",
    "    singular_pep = pep.encodings\n",
    "    singular_extrac_N_and_C = pd.concat([singular_pep.iloc[0][0:8],singular_pep.iloc[0][-8:]],axis=0, ignore_index = True)\n",
    "    # print(singular_pep)\n",
    "    pep_embeddings_collection = pd.concat([pep_embeddings_collection,singular_extrac_N_and_C],axis=1)\n",
    "    # Notice： delete the first row of the output csv, since it is duplicate with the last row"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "outputs": [],
   "source": [
    "pep_embeddings_collection.shape\n",
    "pep_embeddings_collection.T.to_csv('AAIndex_8_features.csv')"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "outputs": [],
   "source": [
    "pep_embeddings_collection = pd.concat([pep_embeddings_collection, singular_extrac_N_and_C], axis=1)"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "outputs": [
    {
     "data": {
      "text/plain": "0     151.00\n1       0.84\n2       5.20\n3       1.81\n4       1.04\n5      13.73\n6     163.00\n7      -0.34\n8     -20.00\n9      -2.50\n10      5.30\n11      0.40\n12      0.49\n13      1.96\n14    121.60\n15      0.19\nName: IAYKP, dtype: float64"
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pep_embeddings_collection = singular_extrac_N_and_C\n",
    "singular_extrac_N_and_C"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "outputs": [
    {
     "data": {
      "text/plain": "AAindex_p.1.BIOV880101    151.00\nAAindex_p.1.BLAM930101      0.84\nAAindex_p.1.CEDJ970104      5.20\nAAindex_p.1.LIFS790101      1.81\nAAindex_p.1.MAXF760101      1.04\nAAindex_p.1.NAKH920108     13.73\nAAindex_p.1.TSAJ990101    163.00\nAAindex_p.1.MIYS990104     -0.34\nAAindex_p.2.BIOV880101     16.00\nAAindex_p.2.BLAM930101      0.96\nAAindex_p.4.TSAJ990101    165.10\nAAindex_p.4.MIYS990104      0.33\nAAindex_p.5.BIOV880101    -20.00\nAAindex_p.5.BLAM930101     -2.50\nAAindex_p.5.CEDJ970104      5.30\nAAindex_p.5.LIFS790101      0.40\nAAindex_p.5.MAXF760101      0.49\nAAindex_p.5.NAKH920108      1.96\nAAindex_p.5.TSAJ990101    121.60\nAAindex_p.5.MIYS990104      0.19\nName: IAYKP, dtype: float64"
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "singular_pep"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "markdown",
   "source": [
    "# full list of features\n",
    "        ----- Available feature types ------\n",
    "\n",
    "        AAC                                                Amino acid composition\n",
    "        EAAC                                               Enhanced amino acid composition\n",
    "        CKSAAP type 1                                      Composition of k-spaced amino acid pairs type 1 - normalized\n",
    "        CKSAAP type 2                                      Composition of k-spaced amino acid pairs type 2 - raw count\n",
    "        DPC type 1                                         Dipeptide composition type 1 - normalized\n",
    "        DPC type 2                                         Dipeptide composition type 2 - raw count\n",
    "        TPC type 1                                         Tripeptide composition type 1 - normalized\n",
    "        TPC type 2                                         Tripeptide composition type 1 - raw count\n",
    "        CTDC                                               Composition\n",
    "        CTDT                                               Transition\n",
    "        CTDD                                               Distribution\n",
    "        CTriad                                             Conjoint triad\n",
    "        KSCTriad                                           Conjoint k-spaced triad\n",
    "        ASDC                                               Adaptive skip dipeptide composition\n",
    "        DistancePair                                       PseAAC of distance-pairs and reduced alphabe\n",
    "        GAAC                                               Grouped amino acid composition\n",
    "        EGAAC                                              Enhanced grouped amino acid composition\n",
    "        CKSAAGP type 1                                     Composition of k-spaced amino acid group pairs type 1- normalized\n",
    "        CKSAAGP type 2                                     Composition of k-spaced amino acid group pairs type 2- raw count\n",
    "        GDPC type 1                                        Grouped dipeptide composition type 1 - normalized\n",
    "        GDPC type 2                                        Grouped dipeptide composition type 2 - raw count\n",
    "        GTPC type 1                                        Grouped tripeptide composition type 1 - normalized\n",
    "        GTPC type 2                                        Grouped tripeptide composition type 1 - raw count\n",
    "        Moran                                              Moran\n",
    "        Geary                                              Geary\n",
    "        NMBroto                                            Normalized Moreau-Broto\n",
    "        AC                                                 Auto covariance\n",
    "        CC                                                 Cross covariance\n",
    "        ACC                                                Auto-cross covariance\n",
    "        SOCNumber                                          Sequence-order-coupling number\n",
    "        QSOrder                                            Quasi-sequence-order descriptors\n",
    "        PAAC                                               Pseudo-amino acid composition\n",
    "        APAAC                                              Amphiphilic PAAC\n",
    "        PseKRAAC type 1                                    Pseudo K-tuple reduced amino acids composition type 1\n",
    "        PseKRAAC type 2                                    Pseudo K-tuple reduced amino acids composition type 2\n",
    "        PseKRAAC type 3A                                   Pseudo K-tuple reduced amino acids composition type 3A\n",
    "        PseKRAAC type 3B                                   Pseudo K-tuple reduced amino acids composition type 3B\n",
    "        PseKRAAC type 4                                    Pseudo K-tuple reduced amino acids composition type 4\n",
    "        PseKRAAC type 5                                    Pseudo K-tuple reduced amino acids composition type 5\n",
    "        PseKRAAC type 6A                                   Pseudo K-tuple reduced amino acids composition type 6A\n",
    "        PseKRAAC type 6B                                   Pseudo K-tuple reduced amino acids composition type 6B\n",
    "        PseKRAAC type 6C                                   Pseudo K-tuple reduced amino acids composition type 6C\n",
    "        PseKRAAC type 7                                    Pseudo K-tuple reduced amino acids composition type 7\n",
    "        PseKRAAC type 8                                    Pseudo K-tuple reduced amino acids composition type 8\n",
    "        PseKRAAC type 9                                    Pseudo K-tuple reduced amino acids composition type 9\n",
    "        PseKRAAC type 10                                   Pseudo K-tuple reduced amino acids composition type 10\n",
    "        PseKRAAC type 11                                   Pseudo K-tuple reduced amino acids composition type 11\n",
    "        PseKRAAC type 12                                   Pseudo K-tuple reduced amino acids composition type 12\n",
    "        PseKRAAC type 13                                   Pseudo K-tuple reduced amino acids composition type 13\n",
    "        PseKRAAC type 14                                   Pseudo K-tuple reduced amino acids composition type 14\n",
    "        PseKRAAC type 15                                   Pseudo K-tuple reduced amino acids composition type 15\n",
    "        PseKRAAC type 16                                   Pseudo K-tuple reduced amino acids composition type 16\n",
    "        binary                                             Binary\n",
    "        binary_6bit                                        Binary\n",
    "        binary_5bit type 1                                 Binary\n",
    "        binary_5bit type 2                                 Binary\n",
    "        binary_3bit type 1                                 Binary\n",
    "        binary_3bit type 2                                 Binary\n",
    "        binary_3bit type 3                                 Binary\n",
    "        binary_3bit type 4                                 Binary\n",
    "        binary_3bit type 5                                 Binary\n",
    "        binary_3bit type 6                                 Binary\n",
    "        binary_3bit type 7                                 Binary\n",
    "        AESNN3                                             Learn from alignments\n",
    "        OPF_10bit                                          Overlapping property features - 10 bit\n",
    "        OPF_7bit type 1                                    Overlapping property features - 7 bit type 1\n",
    "        OPF_7bit type 2                                    Overlapping property features - 7 bit type 2\n",
    "        OPF_7bit type 3                                    Overlapping property features - 7 bit type 3\n",
    "        AAIndex                                            AAIndex\n",
    "        BLOSUM62                                           BLOSUM62\n",
    "        ZScale                                             Z-Scales index\n",
    "        KNN                                                K-nearest neighbor\n",
    "\n",
    "        Note: the first column is the names of availables feature types while the second column is description.\n"
   ],
   "metadata": {
    "collapsed": false
   }
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [],
   "metadata": {
    "collapsed": false
   }
  }
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