top1000_V1.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from io import StringIO\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "file_path = '/Volumes/WD_BLACK/hg38_files/UOK342-YAP1-all.mat'  # Path to the file\n",
    "\n",
    "# Read the contents of the file\n",
    "with open(file_path, 'r') as file:\n",
    "    lines = file.readlines()\n",
    "\n",
    "# Check if the first line starts with \"chr\"\n",
    "if lines and not lines[0].startswith('chr'):\n",
    "    # Remove the first line\n",
    "    lines = lines[1:]\n",
    "\n",
    "# Write the updated contents back to the file\n",
    "with open(file_path, 'w') as file:\n",
    "    file.writelines(lines)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
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       "      <td>chr1</td>\n",
       "      <td>597605</td>\n",
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       "    <tr>\n",
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       "      <td>chr1</td>\n",
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       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_4</td>\n",
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       "      <td>26.0</td>\n",
       "      <td>20.5</td>\n",
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       "      <td>15.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>18.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>371551</th>\n",
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       "      <td>56835608</td>\n",
       "      <td>56835989</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_371552</td>\n",
       "      <td>75.0</td>\n",
       "      <td>.</td>\n",
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       "    <tr>\n",
       "      <th>371552</th>\n",
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       "</table>\n",
       "<p>371553 rows × 1806 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        0         1         2                                         3      \n",
       "0       chr1    597605    598048       UOK121-H3K9me3-rep2_S29.macs_peak_1  \\\n",
       "1       chr1    600262    600534       UOK121-H3K9me3-rep2_S29.macs_peak_2   \n",
       "2       chr1    788709    789095       UOK121-H3K9me3-rep2_S29.macs_peak_3   \n",
       "3       chr1    790091    790363       UOK121-H3K9me3-rep2_S29.macs_peak_4   \n",
       "4       chr1    948493    948765       UOK121-H3K9me3-rep2_S29.macs_peak_5   \n",
       "...      ...       ...       ...                                       ...   \n",
       "371548  chrY  56830020  56830403  UOK121-H3K9me3-rep2_S29.macs_peak_371549   \n",
       "371549  chrY  56832978  56833427  UOK121-H3K9me3-rep2_S29.macs_peak_371550   \n",
       "371550  chrY  56833669  56833941  UOK121-H3K9me3-rep2_S29.macs_peak_371551   \n",
       "371551  chrY  56835608  56835989  UOK121-H3K9me3-rep2_S29.macs_peak_371552   \n",
       "371552  chrY  56856506  56856778  UOK121-H3K9me3-rep2_S29.macs_peak_371553   \n",
       "\n",
       "         4    5     6     7     8     9     ...  1796  1797  1798  1799  1800   \n",
       "0        32.0    .   0.0   0.0   0.0   0.0  ...   0.0   0.0   0.0   0.0   0.0  \\\n",
       "1        32.0    .   0.0   0.0   0.0   0.0  ...   0.0   0.0   0.0   0.0   0.0   \n",
       "2        90.0    .   0.0   0.0   0.0   0.0  ...   0.0   0.0   0.0   0.0   0.0   \n",
       "3        24.0    .   1.0   1.0   1.0   1.0  ...   1.0   1.0   1.0   1.0   1.0   \n",
       "4        13.0    .   0.0   0.0   6.3   7.0  ...   0.0   0.0   0.0   0.0   0.0   \n",
       "...       ...  ...   ...   ...   ...   ...  ...   ...   ...   ...   ...   ...   \n",
       "371548   38.0    .   5.0   5.0   5.0   5.0  ...   6.0   6.0   6.0   6.0   6.0   \n",
       "371549  101.0    .   9.0   9.0   9.0   9.0  ...   6.0   6.0   6.0   6.0   5.0   \n",
       "371550   36.0    .   2.0   2.0   2.0   2.0  ...  26.0  26.0  26.0  26.0  20.5   \n",
       "371551   75.0    .   8.4   8.0   8.0   8.0  ...   0.0   0.0   0.0   0.0   0.0   \n",
       "371552   16.0    .   0.0   0.0   0.0   0.0  ...   0.0   0.0   0.0   0.0   0.0   \n",
       "\n",
       "        1801  1802  1803  1804  1805  \n",
       "0        0.0   0.0   0.0   0.0   0.0  \n",
       "1        0.0   0.0   0.0   0.0   0.0  \n",
       "2        0.0   0.0   0.0   0.0   0.0  \n",
       "3        1.0   1.0   0.3   0.0   0.0  \n",
       "4        0.0   0.0   0.0   0.0   0.0  \n",
       "...      ...   ...   ...   ...   ...  \n",
       "371548   6.0   6.0   6.0   5.7   3.0  \n",
       "371549   1.0   1.0   1.0   1.0   1.2  \n",
       "371550  15.0  15.0  15.0  15.0  18.0  \n",
       "371551   0.0   0.0   0.0   0.0   0.0  \n",
       "371552   0.0   0.0   0.0   0.0   0.0  \n",
       "\n",
       "[371553 rows x 1806 columns]"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "#test if data_transfer is done\n",
    "df = pd.read_csv('/Volumes/WD_BLACK/hg38_files/UOK342-YAP1-all.mat', sep=\"\\t\",header=None)\n",
    "df\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
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       "    <tr>\n",
       "      <th>209668</th>\n",
       "      <td>chr3</td>\n",
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       "    <tr>\n",
       "      <th>33847</th>\n",
       "      <td>chr10</td>\n",
       "      <td>50425463</td>\n",
       "      <td>50425901</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_33848</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356752</th>\n",
       "      <td>chrUn_KI270438v1</td>\n",
       "      <td>109192</td>\n",
       "      <td>109877</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_356753</td>\n",
       "      <td>1813.0</td>\n",
       "      <td>.</td>\n",
       "      <td>19.0</td>\n",
       "      <td>28.6</td>\n",
       "      <td>43.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>...</td>\n",
       "      <td>434.0</td>\n",
       "      <td>312.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>77.4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33094</th>\n",
       "      <td>chr10</td>\n",
       "      <td>41859663</td>\n",
       "      <td>41860329</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_33095</td>\n",
       "      <td>250.0</td>\n",
       "      <td>.</td>\n",
       "      <td>4.2</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.6</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.6</td>\n",
       "      <td>15.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>15.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356799</th>\n",
       "      <td>chrUn_KI270467v1</td>\n",
       "      <td>1007</td>\n",
       "      <td>1523</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_356800</td>\n",
       "      <td>1257.0</td>\n",
       "      <td>.</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>189397</th>\n",
       "      <td>chr21</td>\n",
       "      <td>7258755</td>\n",
       "      <td>7259036</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_189398</td>\n",
       "      <td>226.0</td>\n",
       "      <td>.</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356755</th>\n",
       "      <td>chrUn_KI270438v1</td>\n",
       "      <td>111909</td>\n",
       "      <td>112505</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_356756</td>\n",
       "      <td>1011.0</td>\n",
       "      <td>.</td>\n",
       "      <td>251.0</td>\n",
       "      <td>251.0</td>\n",
       "      <td>251.0</td>\n",
       "      <td>251.0</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>119449</th>\n",
       "      <td>chr16</td>\n",
       "      <td>46390291</td>\n",
       "      <td>46390965</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_119450</td>\n",
       "      <td>1374.0</td>\n",
       "      <td>.</td>\n",
       "      <td>117.0</td>\n",
       "      <td>117.0</td>\n",
       "      <td>137.0</td>\n",
       "      <td>142.0</td>\n",
       "      <td>...</td>\n",
       "      <td>12.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>7.2</td>\n",
       "      <td>6.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356753</th>\n",
       "      <td>chrUn_KI270438v1</td>\n",
       "      <td>110330</td>\n",
       "      <td>110605</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_356754</td>\n",
       "      <td>108.0</td>\n",
       "      <td>.</td>\n",
       "      <td>10.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>7.9</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146313</th>\n",
       "      <td>chr19</td>\n",
       "      <td>17665491</td>\n",
       "      <td>17665933</td>\n",
       "      <td>UOK121-H3K9me3-rep2_S29.macs_peak_146314</td>\n",
       "      <td>124.0</td>\n",
       "      <td>.</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10 rows × 1806 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    0         1         2      \n",
       "209668              chr3  93470319  93470832  \\\n",
       "33847              chr10  50425463  50425901   \n",
       "356752  chrUn_KI270438v1    109192    109877   \n",
       "33094              chr10  41859663  41860329   \n",
       "356799  chrUn_KI270467v1      1007      1523   \n",
       "189397             chr21   7258755   7259036   \n",
       "356755  chrUn_KI270438v1    111909    112505   \n",
       "119449             chr16  46390291  46390965   \n",
       "356753  chrUn_KI270438v1    110330    110605   \n",
       "146313             chr19  17665491  17665933   \n",
       "\n",
       "                                            3        4    5      6      7      \n",
       "209668  UOK121-H3K9me3-rep2_S29.macs_peak_209669  25412.0    .    0.0    0.0  \\\n",
       "33847    UOK121-H3K9me3-rep2_S29.macs_peak_33848   2423.0    .    0.0    0.6   \n",
       "356752  UOK121-H3K9me3-rep2_S29.macs_peak_356753   1813.0    .   19.0   28.6   \n",
       "33094    UOK121-H3K9me3-rep2_S29.macs_peak_33095    250.0    .    4.2    7.0   \n",
       "356799  UOK121-H3K9me3-rep2_S29.macs_peak_356800   1257.0    .    NaN    NaN   \n",
       "189397  UOK121-H3K9me3-rep2_S29.macs_peak_189398    226.0    .    1.0    1.0   \n",
       "356755  UOK121-H3K9me3-rep2_S29.macs_peak_356756   1011.0    .  251.0  251.0   \n",
       "119449  UOK121-H3K9me3-rep2_S29.macs_peak_119450   1374.0    .  117.0  117.0   \n",
       "356753  UOK121-H3K9me3-rep2_S29.macs_peak_356754    108.0    .   10.0   10.0   \n",
       "146313  UOK121-H3K9me3-rep2_S29.macs_peak_146314    124.0    .    0.0    0.0   \n",
       "\n",
       "         8      9     ...   1796   1797   1798   1799   1800   1801  1802   \n",
       "209668    0.0    0.0  ...    0.0    0.0    0.0    0.0    0.0    0.0   0.0  \\\n",
       "33847     3.0    3.0  ...    0.0    0.0    0.0    0.0    0.0    0.0   0.0   \n",
       "356752   43.0   43.0  ...  434.0  312.0  129.0  129.0  129.0  129.0  77.4   \n",
       "33094     7.0    7.0  ...    3.6    4.0    4.0    4.0    4.0   10.6  15.0   \n",
       "356799    NaN    NaN  ...    NaN    NaN    NaN    NaN    NaN    NaN   NaN   \n",
       "189397    1.0    1.0  ...    0.0    0.0    0.0    0.0    0.0    0.0   0.0   \n",
       "356755  251.0  251.0  ...    NaN    NaN    NaN    NaN    NaN    NaN   NaN   \n",
       "119449  137.0  142.0  ...   12.0   12.0    7.2    6.0    6.0    6.0   6.0   \n",
       "356753   10.0    7.9  ...    NaN    NaN    NaN    NaN    NaN    NaN   NaN   \n",
       "146313    0.0    0.0  ...    0.0    0.0    0.0    0.0    0.0    0.0   0.0   \n",
       "\n",
       "        1803  1804  1805  \n",
       "209668   0.5   1.0   1.0  \n",
       "33847    0.0   0.0   0.0  \n",
       "356752   0.0   NaN   NaN  \n",
       "33094   15.0  15.0  15.0  \n",
       "356799   NaN   NaN   NaN  \n",
       "189397   0.0   0.0   0.0  \n",
       "356755   NaN   NaN   NaN  \n",
       "119449   2.0   1.0   1.0  \n",
       "356753   NaN   NaN   NaN  \n",
       "146313   0.0   0.0   0.0  \n",
       "\n",
       "[10 rows x 1806 columns]"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Sort the DataFrame based on column number 4\n",
    "df1 = df\n",
    "df1.sort_values(by=df1.columns[900],ascending=False, inplace=True)\n",
    "df1.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>900</th>\n",
       "      <th>901</th>\n",
       "      <th>902</th>\n",
       "      <th>903</th>\n",
       "      <th>904</th>\n",
       "      <th>905</th>\n",
       "      <th>906</th>\n",
       "      <th>907</th>\n",
       "      <th>908</th>\n",
       "      <th>909</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>33847</th>\n",
       "      <td>3323.0</td>\n",
       "      <td>3323.0</td>\n",
       "      <td>3948.6</td>\n",
       "      <td>6451.0</td>\n",
       "      <td>6451.0</td>\n",
       "      <td>6451.0</td>\n",
       "      <td>6451.0</td>\n",
       "      <td>5787.4</td>\n",
       "      <td>3133.0</td>\n",
       "      <td>3133.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356752</th>\n",
       "      <td>1182.0</td>\n",
       "      <td>1182.0</td>\n",
       "      <td>836.4</td>\n",
       "      <td>318.0</td>\n",
       "      <td>318.0</td>\n",
       "      <td>318.0</td>\n",
       "      <td>318.0</td>\n",
       "      <td>562.4</td>\n",
       "      <td>929.0</td>\n",
       "      <td>929.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33094</th>\n",
       "      <td>1082.0</td>\n",
       "      <td>1050.8</td>\n",
       "      <td>1030.0</td>\n",
       "      <td>1030.0</td>\n",
       "      <td>1030.0</td>\n",
       "      <td>1030.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356799</th>\n",
       "      <td>1059.0</td>\n",
       "      <td>1059.0</td>\n",
       "      <td>1059.0</td>\n",
       "      <td>1059.0</td>\n",
       "      <td>1096.5</td>\n",
       "      <td>1134.0</td>\n",
       "      <td>1134.0</td>\n",
       "      <td>1134.0</td>\n",
       "      <td>1134.0</td>\n",
       "      <td>596.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>189397</th>\n",
       "      <td>991.0</td>\n",
       "      <td>496.5</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>9.5</td>\n",
       "      <td>17.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>17.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356755</th>\n",
       "      <td>752.3</td>\n",
       "      <td>707.0</td>\n",
       "      <td>707.0</td>\n",
       "      <td>707.0</td>\n",
       "      <td>707.0</td>\n",
       "      <td>401.1</td>\n",
       "      <td>270.0</td>\n",
       "      <td>270.0</td>\n",
       "      <td>270.0</td>\n",
       "      <td>270.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>119449</th>\n",
       "      <td>663.0</td>\n",
       "      <td>663.0</td>\n",
       "      <td>663.0</td>\n",
       "      <td>466.2</td>\n",
       "      <td>417.0</td>\n",
       "      <td>417.0</td>\n",
       "      <td>417.0</td>\n",
       "      <td>417.0</td>\n",
       "      <td>863.4</td>\n",
       "      <td>975.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356753</th>\n",
       "      <td>661.0</td>\n",
       "      <td>661.0</td>\n",
       "      <td>661.0</td>\n",
       "      <td>661.0</td>\n",
       "      <td>657.5</td>\n",
       "      <td>656.0</td>\n",
       "      <td>656.0</td>\n",
       "      <td>656.0</td>\n",
       "      <td>656.0</td>\n",
       "      <td>646.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146313</th>\n",
       "      <td>635.0</td>\n",
       "      <td>635.0</td>\n",
       "      <td>635.0</td>\n",
       "      <td>635.0</td>\n",
       "      <td>712.2</td>\n",
       "      <td>1021.0</td>\n",
       "      <td>1021.0</td>\n",
       "      <td>1021.0</td>\n",
       "      <td>1021.0</td>\n",
       "      <td>894.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           900     901     902     903     904     905     906     907   \n",
       "33847   3323.0  3323.0  3948.6  6451.0  6451.0  6451.0  6451.0  5787.4  \\\n",
       "356752  1182.0  1182.0   836.4   318.0   318.0   318.0   318.0   562.4   \n",
       "33094   1082.0  1050.8  1030.0  1030.0  1030.0  1030.0   424.0    20.0   \n",
       "356799  1059.0  1059.0  1059.0  1059.0  1096.5  1134.0  1134.0  1134.0   \n",
       "189397   991.0   496.5     2.0     2.0     2.0     2.0     9.5    17.0   \n",
       "356755   752.3   707.0   707.0   707.0   707.0   401.1   270.0   270.0   \n",
       "119449   663.0   663.0   663.0   466.2   417.0   417.0   417.0   417.0   \n",
       "356753   661.0   661.0   661.0   661.0   657.5   656.0   656.0   656.0   \n",
       "146313   635.0   635.0   635.0   635.0   712.2  1021.0  1021.0  1021.0   \n",
       "\n",
       "           908     909  \n",
       "33847   3133.0  3133.0  \n",
       "356752   929.0   929.0  \n",
       "33094     20.0    20.0  \n",
       "356799  1134.0   596.5  \n",
       "189397    17.0    17.0  \n",
       "356755   270.0   270.0  \n",
       "119449   863.4   975.0  \n",
       "356753   656.0   646.2  \n",
       "146313  1021.0   894.0  "
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df1.iloc[1:10,900:910]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [],
   "source": [
    "top_1000_peaks = df1.head(1000)\n",
    "\n",
    "# Write the top 1000 peaks to a new file\n",
    "top_1000_peaks.to_csv(\"/Volumes/WD_BLACK/hg38_files/top1000.csv\",index=False)"
   ]
  }
 ],
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