SVM_python.ipynb

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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>chr1.1_118328</th>\n",
       "      <th>chr1.1_118386</th>\n",
       "      <th>chr1.1_146744</th>\n",
       "      <th>chr1.1_146745</th>\n",
       "      <th>chr1.1_146748</th>\n",
       "      <th>chr1.1_146813</th>\n",
       "      <th>chr1.1_146845</th>\n",
       "      <th>chr1.1_146992</th>\n",
       "      <th>chr1.1_173569</th>\n",
       "      <th>chr1.1_173638</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>100_S86_R1_001</th>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104_S109_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
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       "    <tr>\n",
       "      <th>107_S121_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108_S40_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>111_S51_R1_001</th>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>112_S63_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113_S75_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115_S87_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>116_S98_R1_001</th>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117_S110_R1_001</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      "text/plain": [
       "                 chr1.1_118328  chr1.1_118386  chr1.1_146744  chr1.1_146745  \\\n",
       "100_S86_R1_001               2              1              1              2   \n",
       "104_S109_R1_001              4              1              0              0   \n",
       "107_S121_R1_001              4              0              0              0   \n",
       "108_S40_R1_001               4              0              1              1   \n",
       "111_S51_R1_001               3              1              0              0   \n",
       "112_S63_R1_001               4              0              3              3   \n",
       "113_S75_R1_001               4              0              1              1   \n",
       "115_S87_R1_001               4              0              1              2   \n",
       "116_S98_R1_001               2              1              0              0   \n",
       "117_S110_R1_001              4              0              0              0   \n",
       "\n",
       "                 chr1.1_146748  chr1.1_146813  chr1.1_146845  chr1.1_146992  \\\n",
       "100_S86_R1_001               1              4              4              4   \n",
       "104_S109_R1_001              0              4              4              3   \n",
       "107_S121_R1_001              2              4              4              3   \n",
       "108_S40_R1_001               1              3              4              4   \n",
       "111_S51_R1_001               0              4              4              4   \n",
       "112_S63_R1_001               3              4              4              3   \n",
       "113_S75_R1_001               1              4              4              2   \n",
       "115_S87_R1_001               2              3              2              3   \n",
       "116_S98_R1_001               3              4              4              4   \n",
       "117_S110_R1_001              3              3              3              4   \n",
       "\n",
       "                 chr1.1_173569  chr1.1_173638  \n",
       "100_S86_R1_001               3              4  \n",
       "104_S109_R1_001              2              4  \n",
       "107_S121_R1_001              2              4  \n",
       "108_S40_R1_001               2              2  \n",
       "111_S51_R1_001               2              4  \n",
       "112_S63_R1_001               3              4  \n",
       "113_S75_R1_001               2              1  \n",
       "115_S87_R1_001               2              1  \n",
       "116_S98_R1_001               2              3  \n",
       "117_S110_R1_001              1              2  "
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     "execution_count": 2,
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   ],
   "source": [
    "# Pandas is used for data manipulation\n",
    "import pandas as pd\n",
    "# Read in data and display first 5 rows\n",
    "features = pd.read_csv('/home/xu/Documents/git/Roza_2019/GS/Roza2019_06_GS.txt', sep = '\\t')\n",
    "features.iloc[:10, :10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
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    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Roza2019_VCF_ID</th>\n",
       "      <th>may_20</th>\n",
       "      <th>jun_20</th>\n",
       "      <th>jul_20</th>\n",
       "      <th>aug_20</th>\n",
       "      <th>sep_20</th>\n",
       "      <th>may_21</th>\n",
       "      <th>jun_21</th>\n",
       "      <th>jul_21</th>\n",
       "      <th>aug_21</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1_S502_R1_001</td>\n",
       "      <td>0.823697</td>\n",
       "      <td>0.791357</td>\n",
       "      <td>0.626798</td>\n",
       "      <td>0.621805</td>\n",
       "      <td>0.361237</td>\n",
       "      <td>0.606106</td>\n",
       "      <td>0.357981</td>\n",
       "      <td>0.487261</td>\n",
       "      <td>0.339005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>4_S444_R1_001</td>\n",
       "      <td>0.824630</td>\n",
       "      <td>0.787806</td>\n",
       "      <td>0.618383</td>\n",
       "      <td>0.646591</td>\n",
       "      <td>0.407386</td>\n",
       "      <td>0.688818</td>\n",
       "      <td>0.472528</td>\n",
       "      <td>0.593768</td>\n",
       "      <td>0.553889</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>5_S1_R1_001</td>\n",
       "      <td>0.833069</td>\n",
       "      <td>0.690481</td>\n",
       "      <td>0.598505</td>\n",
       "      <td>0.556416</td>\n",
       "      <td>0.444338</td>\n",
       "      <td>0.632149</td>\n",
       "      <td>0.438156</td>\n",
       "      <td>0.566734</td>\n",
       "      <td>0.550341</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>6_S6_R1_001</td>\n",
       "      <td>0.746714</td>\n",
       "      <td>0.917990</td>\n",
       "      <td>0.878016</td>\n",
       "      <td>0.646060</td>\n",
       "      <td>0.359331</td>\n",
       "      <td>0.721128</td>\n",
       "      <td>0.405679</td>\n",
       "      <td>0.588227</td>\n",
       "      <td>0.618690</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>7_S456_R1_001</td>\n",
       "      <td>0.659492</td>\n",
       "      <td>0.763600</td>\n",
       "      <td>0.720088</td>\n",
       "      <td>0.573991</td>\n",
       "      <td>0.380440</td>\n",
       "      <td>0.593937</td>\n",
       "      <td>0.393029</td>\n",
       "      <td>0.544851</td>\n",
       "      <td>0.501395</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>9_S11_R1_001</td>\n",
       "      <td>0.838877</td>\n",
       "      <td>0.807992</td>\n",
       "      <td>0.803956</td>\n",
       "      <td>0.724411</td>\n",
       "      <td>0.356564</td>\n",
       "      <td>0.701074</td>\n",
       "      <td>0.379938</td>\n",
       "      <td>0.589005</td>\n",
       "      <td>0.607524</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>12_S468_R1_001</td>\n",
       "      <td>0.745466</td>\n",
       "      <td>0.714092</td>\n",
       "      <td>0.643185</td>\n",
       "      <td>0.677169</td>\n",
       "      <td>0.385896</td>\n",
       "      <td>0.549751</td>\n",
       "      <td>0.407233</td>\n",
       "      <td>0.536713</td>\n",
       "      <td>0.491773</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>13_S16_R1_001</td>\n",
       "      <td>0.679631</td>\n",
       "      <td>0.642564</td>\n",
       "      <td>0.712576</td>\n",
       "      <td>0.689680</td>\n",
       "      <td>0.317458</td>\n",
       "      <td>0.539595</td>\n",
       "      <td>0.349746</td>\n",
       "      <td>0.541915</td>\n",
       "      <td>0.547790</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>14_S20_R1_001</td>\n",
       "      <td>0.775459</td>\n",
       "      <td>0.792291</td>\n",
       "      <td>0.738972</td>\n",
       "      <td>0.748054</td>\n",
       "      <td>0.306401</td>\n",
       "      <td>0.697011</td>\n",
       "      <td>0.363045</td>\n",
       "      <td>0.584912</td>\n",
       "      <td>0.530710</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>15_S24_R1_001</td>\n",
       "      <td>0.793284</td>\n",
       "      <td>0.753322</td>\n",
       "      <td>0.649721</td>\n",
       "      <td>0.604761</td>\n",
       "      <td>0.309925</td>\n",
       "      <td>0.607414</td>\n",
       "      <td>0.296586</td>\n",
       "      <td>0.470989</td>\n",
       "      <td>0.485628</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      ],
      "text/plain": [
       "  Roza2019_VCF_ID    may_20    jun_20    jul_20    aug_20    sep_20    may_21  \\\n",
       "0   1_S502_R1_001  0.823697  0.791357  0.626798  0.621805  0.361237  0.606106   \n",
       "1   4_S444_R1_001  0.824630  0.787806  0.618383  0.646591  0.407386  0.688818   \n",
       "2     5_S1_R1_001  0.833069  0.690481  0.598505  0.556416  0.444338  0.632149   \n",
       "3     6_S6_R1_001  0.746714  0.917990  0.878016  0.646060  0.359331  0.721128   \n",
       "4   7_S456_R1_001  0.659492  0.763600  0.720088  0.573991  0.380440  0.593937   \n",
       "5    9_S11_R1_001  0.838877  0.807992  0.803956  0.724411  0.356564  0.701074   \n",
       "6  12_S468_R1_001  0.745466  0.714092  0.643185  0.677169  0.385896  0.549751   \n",
       "7   13_S16_R1_001  0.679631  0.642564  0.712576  0.689680  0.317458  0.539595   \n",
       "8   14_S20_R1_001  0.775459  0.792291  0.738972  0.748054  0.306401  0.697011   \n",
       "9   15_S24_R1_001  0.793284  0.753322  0.649721  0.604761  0.309925  0.607414   \n",
       "\n",
       "     jun_21    jul_21    aug_21  \n",
       "0  0.357981  0.487261  0.339005  \n",
       "1  0.472528  0.593768  0.553889  \n",
       "2  0.438156  0.566734  0.550341  \n",
       "3  0.405679  0.588227  0.618690  \n",
       "4  0.393029  0.544851  0.501395  \n",
       "5  0.379938  0.589005  0.607524  \n",
       "6  0.407233  0.536713  0.491773  \n",
       "7  0.349746  0.541915  0.547790  \n",
       "8  0.363045  0.584912  0.530710  \n",
       "9  0.296586  0.470989  0.485628  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pheno = pd.read_csv('/home/xu/Documents/git/big_files/BLUE_Yi_sqrt_SpATS_DArT.csv')\n",
    "pheno.iloc[:10, :10]"
   ]
  }
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