publication/scripts/create_assembly_files.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To create the files need for uploading an assembly, all you need is pandas and bioframe (https://bioframe.readthedocs.io/)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import bioframe"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you have an assembly where you can fetch centromeres from the UCSC database via bioframe:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>chrom</th>\n",
       "      <th>start</th>\n",
       "      <th>end</th>\n",
       "      <th>mid</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>chr1</td>\n",
       "      <td>122026459</td>\n",
       "      <td>124932724</td>\n",
       "      <td>123479591</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>chr10</td>\n",
       "      <td>39686682</td>\n",
       "      <td>41593521</td>\n",
       "      <td>40640101</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>chr11</td>\n",
       "      <td>51078348</td>\n",
       "      <td>54425074</td>\n",
       "      <td>52751711</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>chr12</td>\n",
       "      <td>34769407</td>\n",
       "      <td>37185252</td>\n",
       "      <td>35977329</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>chr13</td>\n",
       "      <td>16000000</td>\n",
       "      <td>18051248</td>\n",
       "      <td>17025624</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>chr14</td>\n",
       "      <td>16000000</td>\n",
       "      <td>18173523</td>\n",
       "      <td>17086761</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>chr15</td>\n",
       "      <td>17083673</td>\n",
       "      <td>19725254</td>\n",
       "      <td>18404463</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>chr16</td>\n",
       "      <td>36311158</td>\n",
       "      <td>38265669</td>\n",
       "      <td>37288413</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>chr17</td>\n",
       "      <td>22813679</td>\n",
       "      <td>26616164</td>\n",
       "      <td>24714921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>chr18</td>\n",
       "      <td>15460899</td>\n",
       "      <td>20861206</td>\n",
       "      <td>18161052</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>chr19</td>\n",
       "      <td>24498980</td>\n",
       "      <td>27190874</td>\n",
       "      <td>25844927</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>chr2</td>\n",
       "      <td>92188145</td>\n",
       "      <td>94090557</td>\n",
       "      <td>93139351</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>chr20</td>\n",
       "      <td>26436232</td>\n",
       "      <td>30038348</td>\n",
       "      <td>28237290</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>chr21</td>\n",
       "      <td>10864560</td>\n",
       "      <td>12915808</td>\n",
       "      <td>11890184</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>chr22</td>\n",
       "      <td>12954788</td>\n",
       "      <td>15054318</td>\n",
       "      <td>14004553</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>chr3</td>\n",
       "      <td>90772458</td>\n",
       "      <td>93655574</td>\n",
       "      <td>92214016</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>chr4</td>\n",
       "      <td>49712061</td>\n",
       "      <td>51743951</td>\n",
       "      <td>50728006</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>chr5</td>\n",
       "      <td>46485900</td>\n",
       "      <td>50059807</td>\n",
       "      <td>48272853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>chr6</td>\n",
       "      <td>58553888</td>\n",
       "      <td>59829934</td>\n",
       "      <td>59191911</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>chr7</td>\n",
       "      <td>58169653</td>\n",
       "      <td>61528020</td>\n",
       "      <td>59848836</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>chr8</td>\n",
       "      <td>44033744</td>\n",
       "      <td>45877265</td>\n",
       "      <td>44955504</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>chr9</td>\n",
       "      <td>43389635</td>\n",
       "      <td>45518558</td>\n",
       "      <td>44454096</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>chrX</td>\n",
       "      <td>58605579</td>\n",
       "      <td>62412542</td>\n",
       "      <td>60509060</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>chrY</td>\n",
       "      <td>10316944</td>\n",
       "      <td>10544039</td>\n",
       "      <td>10430491</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    chrom      start        end        mid\n",
       "0    chr1  122026459  124932724  123479591\n",
       "1   chr10   39686682   41593521   40640101\n",
       "2   chr11   51078348   54425074   52751711\n",
       "3   chr12   34769407   37185252   35977329\n",
       "4   chr13   16000000   18051248   17025624\n",
       "5   chr14   16000000   18173523   17086761\n",
       "6   chr15   17083673   19725254   18404463\n",
       "7   chr16   36311158   38265669   37288413\n",
       "8   chr17   22813679   26616164   24714921\n",
       "9   chr18   15460899   20861206   18161052\n",
       "10  chr19   24498980   27190874   25844927\n",
       "11   chr2   92188145   94090557   93139351\n",
       "12  chr20   26436232   30038348   28237290\n",
       "13  chr21   10864560   12915808   11890184\n",
       "14  chr22   12954788   15054318   14004553\n",
       "15   chr3   90772458   93655574   92214016\n",
       "16   chr4   49712061   51743951   50728006\n",
       "17   chr5   46485900   50059807   48272853\n",
       "18   chr6   58553888   59829934   59191911\n",
       "19   chr7   58169653   61528020   59848836\n",
       "20   chr8   44033744   45877265   44955504\n",
       "21   chr9   43389635   45518558   44454096\n",
       "22   chrX   58605579   62412542   60509060\n",
       "23   chrY   10316944   10544039   10430491"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "centromeres = bioframe.fetch_centromeres(\"hg38\")\n",
    "centromeres"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Fetch the sizes:(per default bioframes fetches from the UCSC database)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>0</th>\n",
       "      <td>chr1</td>\n",
       "      <td>248956422</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>chr2</td>\n",
       "      <td>242193529</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>chr3</td>\n",
       "      <td>198295559</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>chr4</td>\n",
       "      <td>190214555</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>chr5</td>\n",
       "      <td>181538259</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>chr6</td>\n",
       "      <td>170805979</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>chr7</td>\n",
       "      <td>159345973</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>chr8</td>\n",
       "      <td>145138636</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>chr9</td>\n",
       "      <td>138394717</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>chr10</td>\n",
       "      <td>133797422</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>chr11</td>\n",
       "      <td>135086622</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>chr12</td>\n",
       "      <td>133275309</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>chr13</td>\n",
       "      <td>114364328</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>chr14</td>\n",
       "      <td>107043718</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>chr15</td>\n",
       "      <td>101991189</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>chr16</td>\n",
       "      <td>90338345</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>chr17</td>\n",
       "      <td>83257441</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>chr18</td>\n",
       "      <td>80373285</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>chr19</td>\n",
       "      <td>58617616</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>chr20</td>\n",
       "      <td>64444167</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>chr21</td>\n",
       "      <td>46709983</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>chr22</td>\n",
       "      <td>50818468</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>chrX</td>\n",
       "      <td>156040895</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>chrY</td>\n",
       "      <td>57227415</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    index     length\n",
       "0    chr1  248956422\n",
       "1    chr2  242193529\n",
       "2    chr3  198295559\n",
       "3    chr4  190214555\n",
       "4    chr5  181538259\n",
       "5    chr6  170805979\n",
       "6    chr7  159345973\n",
       "7    chr8  145138636\n",
       "8    chr9  138394717\n",
       "9   chr10  133797422\n",
       "10  chr11  135086622\n",
       "11  chr12  133275309\n",
       "12  chr13  114364328\n",
       "13  chr14  107043718\n",
       "14  chr15  101991189\n",
       "15  chr16   90338345\n",
       "16  chr17   83257441\n",
       "17  chr18   80373285\n",
       "18  chr19   58617616\n",
       "19  chr20   64444167\n",
       "20  chr21   46709983\n",
       "21  chr22   50818468\n",
       "22   chrX  156040895\n",
       "23   chrY   57227415"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chromsizes = bioframe.fetch_chromsizes(\"hg38\")\n",
    "chromsizes_frame = chromsizes.reset_index().query(\"index != 'chrM'\")\n",
    "chromsizes_frame.to_csv(\"hg38.chrom.sizes\", sep=\"\\t\", header=None, index=False)\n",
    "chromsizes_frame"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now we create the arms out of chromsizes and centromeres."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>chrom</th>\n",
       "      <th>start</th>\n",
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       "  <tbody>\n",
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       "      <th>1</th>\n",
       "      <td>chr1</td>\n",
       "      <td>123479591</td>\n",
       "      <td>248956422</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>chr2</td>\n",
       "      <td>0</td>\n",
       "      <td>93139351</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>chr2</td>\n",
       "      <td>93139351</td>\n",
       "      <td>242193529</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>chr3</td>\n",
       "      <td>0</td>\n",
       "      <td>92214016</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>chr3</td>\n",
       "      <td>92214016</td>\n",
       "      <td>198295559</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>chr4</td>\n",
       "      <td>0</td>\n",
       "      <td>50728006</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>chr4</td>\n",
       "      <td>50728006</td>\n",
       "      <td>190214555</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>chr5</td>\n",
       "      <td>0</td>\n",
       "      <td>48272853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>chr5</td>\n",
       "      <td>48272853</td>\n",
       "      <td>181538259</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>chr6</td>\n",
       "      <td>0</td>\n",
       "      <td>59191911</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>chr6</td>\n",
       "      <td>59191911</td>\n",
       "      <td>170805979</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>chr7</td>\n",
       "      <td>0</td>\n",
       "      <td>59848836</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>chr7</td>\n",
       "      <td>59848836</td>\n",
       "      <td>159345973</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>chr8</td>\n",
       "      <td>0</td>\n",
       "      <td>44955504</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>chr8</td>\n",
       "      <td>44955504</td>\n",
       "      <td>145138636</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>chr9</td>\n",
       "      <td>0</td>\n",
       "      <td>44454096</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>chr9</td>\n",
       "      <td>44454096</td>\n",
       "      <td>138394717</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>chr10</td>\n",
       "      <td>0</td>\n",
       "      <td>40640101</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>chr10</td>\n",
       "      <td>40640101</td>\n",
       "      <td>133797422</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>chr11</td>\n",
       "      <td>0</td>\n",
       "      <td>52751711</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>chr11</td>\n",
       "      <td>52751711</td>\n",
       "      <td>135086622</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>chr12</td>\n",
       "      <td>0</td>\n",
       "      <td>35977329</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>chr12</td>\n",
       "      <td>35977329</td>\n",
       "      <td>133275309</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>chr13</td>\n",
       "      <td>0</td>\n",
       "      <td>17025624</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>chr13</td>\n",
       "      <td>17025624</td>\n",
       "      <td>114364328</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>chr14</td>\n",
       "      <td>0</td>\n",
       "      <td>17086761</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>chr14</td>\n",
       "      <td>17086761</td>\n",
       "      <td>107043718</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>chr15</td>\n",
       "      <td>0</td>\n",
       "      <td>18404463</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>chr15</td>\n",
       "      <td>18404463</td>\n",
       "      <td>101991189</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>chr16</td>\n",
       "      <td>0</td>\n",
       "      <td>37288413</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>chr16</td>\n",
       "      <td>37288413</td>\n",
       "      <td>90338345</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>chr17</td>\n",
       "      <td>0</td>\n",
       "      <td>24714921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>chr17</td>\n",
       "      <td>24714921</td>\n",
       "      <td>83257441</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>chr18</td>\n",
       "      <td>0</td>\n",
       "      <td>18161052</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>chr18</td>\n",
       "      <td>18161052</td>\n",
       "      <td>80373285</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>chr19</td>\n",
       "      <td>0</td>\n",
       "      <td>25844927</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>chr19</td>\n",
       "      <td>25844927</td>\n",
       "      <td>58617616</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>chr20</td>\n",
       "      <td>0</td>\n",
       "      <td>28237290</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>chr20</td>\n",
       "      <td>28237290</td>\n",
       "      <td>64444167</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>chr21</td>\n",
       "      <td>0</td>\n",
       "      <td>11890184</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>chr21</td>\n",
       "      <td>11890184</td>\n",
       "      <td>46709983</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>chr22</td>\n",
       "      <td>0</td>\n",
       "      <td>14004553</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>chr22</td>\n",
       "      <td>14004553</td>\n",
       "      <td>50818468</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>chrX</td>\n",
       "      <td>0</td>\n",
       "      <td>60509060</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>chrX</td>\n",
       "      <td>60509060</td>\n",
       "      <td>156040895</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>chrY</td>\n",
       "      <td>0</td>\n",
       "      <td>10430491</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>chrY</td>\n",
       "      <td>10430491</td>\n",
       "      <td>57227415</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>chrM</td>\n",
       "      <td>0</td>\n",
       "      <td>16569</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    chrom      start        end\n",
       "0    chr1          0  123479591\n",
       "1    chr1  123479591  248956422\n",
       "2    chr2          0   93139351\n",
       "3    chr2   93139351  242193529\n",
       "4    chr3          0   92214016\n",
       "5    chr3   92214016  198295559\n",
       "6    chr4          0   50728006\n",
       "7    chr4   50728006  190214555\n",
       "8    chr5          0   48272853\n",
       "9    chr5   48272853  181538259\n",
       "10   chr6          0   59191911\n",
       "11   chr6   59191911  170805979\n",
       "12   chr7          0   59848836\n",
       "13   chr7   59848836  159345973\n",
       "14   chr8          0   44955504\n",
       "15   chr8   44955504  145138636\n",
       "16   chr9          0   44454096\n",
       "17   chr9   44454096  138394717\n",
       "18  chr10          0   40640101\n",
       "19  chr10   40640101  133797422\n",
       "20  chr11          0   52751711\n",
       "21  chr11   52751711  135086622\n",
       "22  chr12          0   35977329\n",
       "23  chr12   35977329  133275309\n",
       "24  chr13          0   17025624\n",
       "25  chr13   17025624  114364328\n",
       "26  chr14          0   17086761\n",
       "27  chr14   17086761  107043718\n",
       "28  chr15          0   18404463\n",
       "29  chr15   18404463  101991189\n",
       "30  chr16          0   37288413\n",
       "31  chr16   37288413   90338345\n",
       "32  chr17          0   24714921\n",
       "33  chr17   24714921   83257441\n",
       "34  chr18          0   18161052\n",
       "35  chr18   18161052   80373285\n",
       "36  chr19          0   25844927\n",
       "37  chr19   25844927   58617616\n",
       "38  chr20          0   28237290\n",
       "39  chr20   28237290   64444167\n",
       "40  chr21          0   11890184\n",
       "41  chr21   11890184   46709983\n",
       "42  chr22          0   14004553\n",
       "43  chr22   14004553   50818468\n",
       "44   chrX          0   60509060\n",
       "45   chrX   60509060  156040895\n",
       "46   chrY          0   10430491\n",
       "47   chrY   10430491   57227415\n",
       "48   chrM          0      16569"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "arms = bioframe.make_chromarms(chromsizes, centromeres)\n",
    "arms[['chrom','start','end']].to_csv('arms.hg38',index=False)\n",
    "arms[['chrom','start','end']]"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If centromeres can not be fetched for our genome:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>chrom</th>\n",
       "      <th>start</th>\n",
       "      <th>end</th>\n",
       "      <th>mid</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [chrom, start, end, mid]\n",
       "Index: []"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "centromeres = bioframe.fetch_centromeres(\"mm9\")\n",
    "centromeres"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can simply take the midpoint as centromeres, since we only use the arms for optimization purposes.\n",
    "\n",
    "_Future version of HiCognition might only need the chromsizes._"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "chromsizes = bioframe.fetch_chromsizes(\"mm9\")\n",
    "chromsizes_frame = chromsizes.reset_index().query(\"index != 'chrM'\")\n",
    "\n",
    "chromsizes_frame.to_csv(\"mm9.chrom.sizes\", sep=\"\\t\", header=None, index=False)\n",
    "\n",
    "# take center as centromeres\n",
    "centromeres = chromsizes//2\n",
    "\n",
    "\n",
    "arms = [\n",
    "    arm\n",
    "    for chrom in chromsizes_frame[\"index\"]\n",
    "    for arm in (\n",
    "        (chrom, 0, centromeres.get(chrom, 0)),\n",
    "        (chrom, centromeres.get(chrom, 0), chromsizes.get(chrom, 0)),\n",
    "    )\n",
    "]\n",
    "\n",
    "# construct dataframe out of arms\n",
    "arms = pd.DataFrame(arms, columns=[\"chrom\", \"start\", \"end\"])\n",
    "\n",
    "arms.to_csv(\"arms.mm9\", index=False)"
   ]
  }
 ],
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