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joshmoore/gene_identifier.ipynb

Last active February 2, 2016 15:26
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gene_identifier.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from pandas import *"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"df = read_csv(\"../data/out.tsv\", delimiter=\"\\t\")"
]
},
{
"cell_type": "code",
"execution_count": 79,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"counts = df.apply(lambda it: len([x for x in it if x])-1, axis=1)"
]
},
{
"cell_type": "code",
"execution_count": 80,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"counts.name = \"Counts\""
]
},
{
"cell_type": "code",
"execution_count": 81,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"full = df.join(counts)"
]
},
{
"cell_type": "code",
"execution_count": 82,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>16</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23303</th>\n",
" <td>10870</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>16</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23304</th>\n",
" <td>10875</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>32</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23305</th>\n",
" <td>10874</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>16</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23306</th>\n",
" <td>10876</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>28</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23308</th>\n",
" <td>YKL010C</td>\n",
" <td>15</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23309</th>\n",
" <td>ENSG00000178996</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>12</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23310</th>\n",
" <td>ENSG00000178997</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>0</td>\n",
" <td>12</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23311</th>\n",
" <td>ENSG00000178999</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>16</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23312</th>\n",
" <td>YGR013W</td>\n",
" <td>15</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23313</th>\n",
" <td>SPCC306.05c</td>\n",
" <td>0</td>\n",
" <td>12</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23314</th>\n",
" <td>ENSG00000179029</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>14</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23315</th>\n",
" <td>ENSG00000145283</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>21</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23318</th>\n",
" <td>ENSG00000179023</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>18</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23319</th>\n",
" <td>FBgn0028552</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23321</th>\n",
" <td>ENSG00000250907</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23322</th>\n",
" <td>FBgn0259937</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>2</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23323</th>\n",
" <td>ENSG00000091844</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>21</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23324</th>\n",
" <td>SPAC18B11.04</td>\n",
" <td>0</td>\n",
" <td>12</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
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" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23326</th>\n",
" <td>FBgn0087008</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23327</th>\n",
" <td>ENSG00000156162</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>6</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23328</th>\n",
" <td>ENSG00000071553</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>0</td>\n",
" <td>37</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23329</th>\n",
" <td>FBgn0034400</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23330</th>\n",
" <td>FBgn0039448</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>66815</th>\n",
" <td>YPL013C</td>\n",
" <td>15</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>66816 rows × 14 columns</p>\n",
"</div>"
],
"text/plain": [
" Gene Identifier 51 3 102 201 202 206 751 803 \\\n",
"48847 YPR008W 15 0 0 9 1 0 0 0 \n",
"5222 YJL053W 15 0 0 9 1 0 0 0 \n",
"34232 YDR345C 15 0 0 9 1 0 0 0 \n",
"19264 YOR014W 15 0 0 9 1 0 0 0 \n",
"39609 YLR346C 15 0 0 9 1 0 0 0 \n",
"66397 YOR332W 15 0 0 9 1 0 0 0 \n",
"14153 YOR374W 15 0 0 9 1 0 0 0 \n",
"53247 YGL163C 15 0 0 9 1 0 0 0 \n",
"919 YFR015C 15 0 0 9 1 0 0 0 \n",
"15889 YDR171W 15 0 0 9 1 0 0 0 \n",
"25958 YJL145W 15 0 0 9 1 0 0 0 \n",
"65332 YPL074W 15 0 0 9 1 0 0 0 \n",
"6511 YNL242W 15 0 0 9 1 0 0 0 \n",
"39599 YMR037C 15 0 0 9 1 0 0 0 \n",
"66645 YOL151W 15 0 0 9 2 0 0 0 \n",
"44405 YML027W 15 0 0 9 1 0 0 0 \n",
"58021 YGR086C 15 0 0 9 1 0 0 0 \n",
"11934 YDR129C 15 0 0 9 1 0 0 0 \n",
"18964 YMR056C 15 0 0 9 1 0 0 0 \n",
"60952 YNL211C 15 0 0 9 1 0 0 0 \n",
"41046 YOR188W 15 0 0 9 1 0 0 0 \n",
"8046 YNL175C 15 0 0 9 1 0 0 0 \n",
"14174 YKR010C 15 0 0 9 1 0 0 0 \n",
"33931 YNL058C 15 0 0 9 1 0 0 0 \n",
"20082 YIL087C 15 0 0 9 1 0 0 0 \n",
"22301 YDL059C 15 0 0 9 1 0 0 0 \n",
"26007 YAR014C 15 0 0 9 1 0 0 0 \n",
"43174 YNL147W 15 0 0 9 1 0 0 0 \n",
"29038 YER088C 15 0 0 9 1 0 0 0 \n",
"42288 YMR267W 15 0 0 9 1 0 0 0 \n",
"... ... .. .. ... ... ... ... ... ... \n",
"23297 10879 0 0 0 0 0 0 0 0 \n",
"23331 FBgn0034403 0 0 0 0 0 0 0 0 \n",
"23298 10878 0 0 0 0 0 0 0 0 \n",
"23299 FBgn0033767 0 0 0 0 0 0 0 0 \n",
"23300 ENSG00000169059 0 0 0 0 0 0 0 0 \n",
"23302 10871 0 0 0 0 0 0 0 0 \n",
"23303 10870 0 0 0 0 0 0 0 0 \n",
"23304 10875 0 0 0 0 0 0 0 0 \n",
"23305 10874 0 0 0 0 0 0 0 0 \n",
"23306 10876 0 0 0 0 0 0 0 0 \n",
"23308 YKL010C 15 0 0 0 0 0 0 0 \n",
"23309 ENSG00000178996 0 0 0 0 0 0 0 0 \n",
"23310 ENSG00000178997 0 0 0 0 0 0 0 0 \n",
"23311 ENSG00000178999 0 0 0 0 0 0 0 0 \n",
"23312 YGR013W 15 0 0 0 0 0 0 0 \n",
"23313 SPCC306.05c 0 12 0 0 0 0 0 0 \n",
"23314 ENSG00000179029 0 0 0 0 0 0 0 0 \n",
"23315 ENSG00000145283 0 0 0 0 0 0 0 0 \n",
"23318 ENSG00000179023 0 0 0 0 0 0 0 0 \n",
"23319 FBgn0028552 0 0 0 0 0 0 0 0 \n",
"23321 ENSG00000250907 0 0 2 0 0 0 0 0 \n",
"23322 FBgn0259937 0 0 0 0 0 0 0 0 \n",
"23323 ENSG00000091844 0 0 0 0 0 0 0 0 \n",
"23324 SPAC18B11.04 0 12 0 0 0 0 0 0 \n",
"23326 FBgn0087008 0 0 0 0 0 0 0 0 \n",
"23327 ENSG00000156162 0 0 0 0 0 0 0 0 \n",
"23328 ENSG00000071553 0 0 0 0 0 0 0 0 \n",
"23329 FBgn0034400 0 0 0 0 0 0 0 0 \n",
"23330 FBgn0039448 0 0 0 0 0 0 0 0 \n",
"66815 YPL013C 15 0 0 0 0 0 0 0 \n",
"\n",
" 597 154 251 253 Counts \n",
"48847 0 0 0 0 3 \n",
"5222 0 0 0 0 3 \n",
"34232 0 0 0 0 3 \n",
"19264 0 0 0 0 3 \n",
"39609 0 0 0 0 3 \n",
"66397 0 0 0 0 3 \n",
"14153 0 0 0 0 3 \n",
"53247 0 0 0 0 3 \n",
"919 0 0 0 0 3 \n",
"15889 0 0 0 0 3 \n",
"25958 0 0 0 0 3 \n",
"65332 0 0 0 0 3 \n",
"6511 0 0 0 0 3 \n",
"39599 0 0 0 0 3 \n",
"66645 0 0 0 0 3 \n",
"44405 0 0 0 0 3 \n",
"58021 0 0 0 0 3 \n",
"11934 0 0 0 0 3 \n",
"18964 0 0 0 0 3 \n",
"60952 0 0 0 0 3 \n",
"41046 0 0 0 0 3 \n",
"8046 0 0 0 0 3 \n",
"14174 0 0 0 0 3 \n",
"33931 0 0 0 0 3 \n",
"20082 0 0 0 0 3 \n",
"22301 0 0 0 0 3 \n",
"26007 0 0 0 0 3 \n",
"43174 0 0 0 0 3 \n",
"29038 0 0 0 0 3 \n",
"42288 0 0 0 0 3 \n",
"... ... ... ... ... ... \n",
"23297 0 0 0 16 1 \n",
"23331 0 2 0 0 1 \n",
"23298 0 0 0 16 1 \n",
"23299 0 2 0 0 1 \n",
"23300 0 0 6 0 1 \n",
"23302 0 0 0 16 1 \n",
"23303 0 0 0 16 1 \n",
"23304 0 0 0 32 1 \n",
"23305 0 0 0 16 1 \n",
"23306 0 0 0 28 1 \n",
"23308 0 0 0 0 1 \n",
"23309 0 0 12 0 1 \n",
"23310 0 0 12 0 1 \n",
"23311 0 0 16 0 1 \n",
"23312 0 0 0 0 1 \n",
"23313 0 0 0 0 1 \n",
"23314 0 0 14 0 1 \n",
"23315 0 0 21 0 1 \n",
"23318 0 0 18 0 1 \n",
"23319 0 2 0 0 1 \n",
"23321 0 0 0 0 1 \n",
"23322 0 2 0 0 1 \n",
"23323 0 0 21 0 1 \n",
"23324 0 0 0 0 1 \n",
"23326 0 2 0 0 1 \n",
"23327 0 0 6 0 1 \n",
"23328 0 0 37 0 1 \n",
"23329 0 2 0 0 1 \n",
"23330 0 2 0 0 1 \n",
"66815 0 0 0 0 1 \n",
"\n",
"[66816 rows x 14 columns]"
]
},
"execution_count": 82,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"full.sort(\"Counts\", ascending=False)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 0
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