{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Single-cell cooler format Python API examples"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The here provided examples are using the cooler Python API with version 0.8.9. Earlier versions do not support single-cell cooler files.\n",
    "The single-cell cooler format uses an HDF5 container and can therefore be accessed with any HDF5 library of any programming language. However, the programmer needs to take care of all the operations on his/her own and make sure the single-cell cooler definitions are met. \n",
    "Please consider our documentation on https://cooler.readthedocs.io/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import cooler\n",
    "import os"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Create a single-cell cooler file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Load cooler files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "path_file1 = 'data/single-cell/GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "path_file2 = 'data/single-cell/GSM2687249_41670_GGCTAC-R1-DpnII.100000.cool'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "path_file3 = 'data/single-cell/GSM2687250_41671_TTAGGC-R1-DpnII.100000.cool'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooler_file1 = cooler.Cooler(path_file1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooler_file2 = cooler.Cooler(path_file2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooler_file3 = cooler.Cooler(path_file3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Load pixels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "pixel1 = cooler_file1.pixels()[:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "pixel2 = cooler_file2.pixels()[:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "pixel3 = cooler_file3.pixels()[:]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Load bins"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "bin1 = cooler_file1.bins()[:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "bin2 = cooler_file2.bins()[:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "bin3 = cooler_file3.bins()[:]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Cell names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "cell_name_list = [os.path.basename(cooler_file1.filename), os.path.basename(cooler_file2.filename), os.path.basename(cooler_file3.filename)]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Create input"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Bins either as pandas pixels or as a dict of name:bins (as pandas pixels)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "bins = bin1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "bins_dictionary = {cell_name_list[0]:bin1, cell_name_list[1]:bin2, cell_name_list[2]:bin3}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Pixels as dictionary name:pixels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "pixels_dictionary = {cell_name_list[0]:pixel1, cell_name_list[1]:pixel2, cell_name_list[2]:pixel3}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Create scool with bins as pandas dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/nezar/miniconda3/lib/python3.7/site-packages/dask/dataframe/utils.py:15: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.\n",
      "  import pandas.util.testing as tm\n"
     ]
    }
   ],
   "source": [
    "cooler.create_scool('outfile_test.scool', bins, pixels_dictionary)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Create scool with bins as dictonary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooler.create_scool('outfile_test.scool', bins_dictionary, pixels_dictionary)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read scool"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get paths of the cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "content_of_scool = cooler.fileops.list_scool_cells('outfile_test.scool')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['/cells/GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool',\n",
       " '/cells/GSM2687249_41670_GGCTAC-R1-DpnII.100000.cool',\n",
       " '/cells/GSM2687250_41671_TTAGGC-R1-DpnII.100000.cool']"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "content_of_scool"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load the individual cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "cell1 = cooler.Cooler('outfile_test.scool' + '::' + content_of_scool[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "cell2 = cooler.Cooler('outfile_test.scool' + '::' + content_of_scool[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "cell3 = cooler.Cooler('outfile_test.scool' + '::' + content_of_scool[2])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Bin content"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The bins are shared and for all cells identical"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>3</th>\n",
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       "      <td>500000</td>\n",
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       "      <th>5</th>\n",
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       "      <td>500000</td>\n",
       "      <td>600000</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>1</td>\n",
       "      <td>600000</td>\n",
       "      <td>700000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1</td>\n",
       "      <td>700000</td>\n",
       "      <td>800000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>1</td>\n",
       "      <td>800000</td>\n",
       "      <td>900000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>1</td>\n",
       "      <td>900000</td>\n",
       "      <td>1000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  chrom   start      end\n",
       "0     1       0   100000\n",
       "1     1  100000   200000\n",
       "2     1  200000   300000\n",
       "3     1  300000   400000\n",
       "4     1  400000   500000\n",
       "5     1  500000   600000\n",
       "6     1  600000   700000\n",
       "7     1  700000   800000\n",
       "8     1  800000   900000\n",
       "9     1  900000  1000000"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cell1.bins()[:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>5</th>\n",
       "      <td>1</td>\n",
       "      <td>500000</td>\n",
       "      <td>600000</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>1</td>\n",
       "      <td>600000</td>\n",
       "      <td>700000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1</td>\n",
       "      <td>700000</td>\n",
       "      <td>800000</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>1</td>\n",
       "      <td>800000</td>\n",
       "      <td>900000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>1</td>\n",
       "      <td>900000</td>\n",
       "      <td>1000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  chrom   start      end\n",
       "0     1       0   100000\n",
       "1     1  100000   200000\n",
       "2     1  200000   300000\n",
       "3     1  300000   400000\n",
       "4     1  400000   500000\n",
       "5     1  500000   600000\n",
       "6     1  600000   700000\n",
       "7     1  700000   800000\n",
       "8     1  800000   900000\n",
       "9     1  900000  1000000"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cell2.bins()[:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>5</th>\n",
       "      <td>1</td>\n",
       "      <td>500000</td>\n",
       "      <td>600000</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>1</td>\n",
       "      <td>600000</td>\n",
       "      <td>700000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1</td>\n",
       "      <td>700000</td>\n",
       "      <td>800000</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>1</td>\n",
       "      <td>800000</td>\n",
       "      <td>900000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>1</td>\n",
       "      <td>900000</td>\n",
       "      <td>1000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  chrom   start      end\n",
       "0     1       0   100000\n",
       "1     1  100000   200000\n",
       "2     1  200000   300000\n",
       "3     1  300000   400000\n",
       "4     1  400000   500000\n",
       "5     1  500000   600000\n",
       "6     1  600000   700000\n",
       "7     1  700000   800000\n",
       "8     1  800000   900000\n",
       "9     1  900000  1000000"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cell3.bins()[:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Pixel content"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The content of the pixels are in all cells different"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>31</td>\n",
       "      <td>31</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>32</td>\n",
       "      <td>32</td>\n",
       "      <td>12</td>\n",
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       "      <th>6</th>\n",
       "      <td>32</td>\n",
       "      <td>33</td>\n",
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       "      <th>7</th>\n",
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       "      <td>35</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>32</td>\n",
       "      <td>16190</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>32</td>\n",
       "      <td>17939</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      ],
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       "   bin1_id  bin2_id  count\n",
       "0       30       30      1\n",
       "1       30      901      1\n",
       "2       30    11424      1\n",
       "3       30    12923      1\n",
       "4       31       31      2\n",
       "5       32       32     12\n",
       "6       32       33      1\n",
       "7       32       35      1\n",
       "8       32    16190      1\n",
       "9       32    17939      1"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
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   "source": [
    "cell1.pixels()[:10]"
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  },
  {
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   "execution_count": 29,
   "metadata": {},
   "outputs": [
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       "   bin1_id  bin2_id  count\n",
       "0       32      277      1\n",
       "1       33       33      1\n",
       "2       33    25964      2\n",
       "3       34       34      1\n",
       "4       34       37      2\n",
       "5       34       49      2\n",
       "6       35       35     12\n",
       "7       35       36      2\n",
       "8       35     5992      1\n",
       "9       35     8914      1"
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     "metadata": {},
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   "source": [
    "cell2.pixels()[:10]"
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  {
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   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
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       "      <td>31</td>\n",
       "      <td>53</td>\n",
       "      <td>6</td>\n",
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       "      <th>7</th>\n",
       "      <td>31</td>\n",
       "      <td>54</td>\n",
       "      <td>5</td>\n",
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       "      <th>8</th>\n",
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       "   bin1_id  bin2_id  count\n",
       "0       30       30      4\n",
       "1       30     4486      1\n",
       "2       30     9079      1\n",
       "3       30    16001      1\n",
       "4       31       31      4\n",
       "5       31       32      2\n",
       "6       31       53      6\n",
       "7       31       54      5\n",
       "8       31      190      1\n",
       "9       31    23253      1"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
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   "source": [
    "cell3.pixels()[:10]"
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