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Created February 2, 2016 16:52
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tops.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from pandas import *"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"gene = read_csv(\"../data/gene.tsv\", delimiter=\"\\t\")"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>gene</th>\n",
" <th>idr0001-</th>\n",
" <th>idr0002-</th>\n",
" <th>idr0003-</th>\n",
" <th>idr0004-</th>\n",
" <th>idr0005-</th>\n",
" <th>idr0006-</th>\n",
" <th>idr0007-</th>\n",
" <th>idr0008-</th>\n",
" <th>idr0009-</th>\n",
" <th>idr0013-</th>\n",
" <th>Screens</th>\n",
" <th>Images</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>5353</th>\n",
" <td>YJL053W ...</td>\n",
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" <td>25</td>\n",
" </tr>\n",
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" <th>37602</th>\n",
" <td>YJL092W ...</td>\n",
" <td>0</td>\n",
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" <td>32</td>\n",
" </tr>\n",
" <tr>\n",
" <th>62020</th>\n",
" <td>YDL134C ...</td>\n",
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" <td>25</td>\n",
" </tr>\n",
" <tr>\n",
" <th>47864</th>\n",
" <td>YLL026W ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>9</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
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" <td>3</td>\n",
" <td>25</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30054</th>\n",
" <td>YGL131C ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>9</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>3</td>\n",
" <td>25</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" gene idr0001- idr0002- \\\n",
"5353 YJL053W ... 0 0 \n",
"44352 ENSG00000066455 ... 0 10 \n",
"35843 YDR169C ... 0 0 \n",
"37602 YJL092W ... 0 0 \n",
"5990 ENSG00000132341 ... 0 7 \n",
"24976 YLR393W ... 0 0 \n",
"5998 ENSG00000010256 ... 0 7 \n",
"62020 YDL134C ... 0 0 \n",
"47864 YLL026W ... 0 0 \n",
"30054 YGL131C ... 0 0 \n",
"\n",
" idr0003- idr0004- idr0005- idr0006- idr0007- idr0008- idr0009- \\\n",
"5353 15 1 0 0 9 0 0 \n",
"44352 0 0 0 0 0 0 14 \n",
"35843 15 1 0 0 9 0 0 \n",
"37602 15 1 0 0 9 0 0 \n",
"5990 0 0 0 0 0 0 12 \n",
"24976 15 1 0 0 9 0 0 \n",
"5998 0 0 0 0 0 0 16 \n",
"62020 15 1 0 0 9 0 0 \n",
"47864 15 1 0 0 9 0 0 \n",
"30054 15 1 0 0 9 0 0 \n",
"\n",
" idr0013- Screens Images \n",
"5353 0 3 25 \n",
"44352 6 3 30 \n",
"35843 0 3 25 \n",
"37602 0 3 25 \n",
"5990 6 3 25 \n",
"24976 0 3 25 \n",
"5998 9 3 32 \n",
"62020 0 3 25 \n",
"47864 0 3 25 \n",
"30054 0 3 25 "
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"gene.sort(\"Screens\", ascending=False)[0:10]"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"symbol = read_csv(\"../data/symbol.tsv\", delimiter=\"\\t\")"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>symbol</th>\n",
" <th>idr0001-</th>\n",
" <th>idr0002-</th>\n",
" <th>idr0003-</th>\n",
" <th>idr0004-</th>\n",
" <th>idr0005-</th>\n",
" <th>idr0006-</th>\n",
" <th>idr0007-</th>\n",
" <th>idr0008-</th>\n",
" <th>idr0009-</th>\n",
" <th>idr0013-</th>\n",
" <th>Screens</th>\n",
" <th>Images</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>2625</th>\n",
" <td>EDC3 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
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" <tr>\n",
" <th>38223</th>\n",
" <td>ACE2 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
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" <td>10</td>\n",
" <td>5</td>\n",
" <td>47</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18589</th>\n",
" <td>MED1 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>0</td>\n",
" <td>3</td>\n",
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" <td>0</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" <td>6</td>\n",
" <td>5</td>\n",
" <td>54</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18590</th>\n",
" <td>MED6 ...</td>\n",
" <td>0</td>\n",
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" <td>15</td>\n",
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" <td>5</td>\n",
" <td>5</td>\n",
" <td>41</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18591</th>\n",
" <td>MED7 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>0</td>\n",
" <td>3</td>\n",
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" <td>0</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
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" <td>5</td>\n",
" <td>44</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18592</th>\n",
" <td>MED4 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>0</td>\n",
" <td>3</td>\n",
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" <td>5</td>\n",
" <td>5</td>\n",
" <td>41</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32725</th>\n",
" <td>VPS41 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
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" <td>5</td>\n",
" <td>49</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18593</th>\n",
" <td>MED8 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
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" <td>3</td>\n",
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" <td>5</td>\n",
" <td>45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14790</th>\n",
" <td>REV1 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>12</td>\n",
" <td>9</td>\n",
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" <td>10</td>\n",
" <td>5</td>\n",
" <td>47</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20662</th>\n",
" <td>RAD50 ...</td>\n",
" <td>0</td>\n",
" <td>9</td>\n",
" <td>15</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
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" <td>0</td>\n",
" <td>9</td>\n",
" <td>5</td>\n",
" <td>44</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" symbol idr0001- idr0002- \\\n",
"2625 EDC3 ... 0 0 \n",
"38223 ACE2 ... 0 0 \n",
"18589 MED1 ... 0 0 \n",
"18590 MED6 ... 0 0 \n",
"18591 MED7 ... 0 0 \n",
"18592 MED4 ... 0 0 \n",
"32725 VPS41 ... 0 0 \n",
"18593 MED8 ... 0 0 \n",
"14790 REV1 ... 0 0 \n",
"20662 RAD50 ... 0 9 \n",
"\n",
" idr0003- idr0004- idr0005- idr0006- idr0007- idr0008- idr0009- \\\n",
"2625 15 1 0 16 9 0 0 \n",
"38223 15 1 0 12 9 0 0 \n",
"18589 15 0 3 28 0 2 0 \n",
"18590 15 0 3 16 0 2 0 \n",
"18591 15 0 3 16 0 2 0 \n",
"18592 15 0 3 16 0 2 0 \n",
"32725 15 1 0 16 9 0 0 \n",
"18593 15 0 3 16 0 2 0 \n",
"14790 15 1 0 12 9 0 0 \n",
"20662 15 2 0 0 9 0 0 \n",
"\n",
" idr0013- Screens Images \n",
"2625 8 5 49 \n",
"38223 10 5 47 \n",
"18589 6 5 54 \n",
"18590 5 5 41 \n",
"18591 8 5 44 \n",
"18592 5 5 41 \n",
"32725 8 5 49 \n",
"18593 9 5 45 \n",
"14790 10 5 47 \n",
"20662 9 5 44 "
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"symbol.sort(\"Screens\", ascending=False)[0:10]"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"phenotype = read_csv(\"../data/phenotype.tsv\", delimiter=\"\\t\")"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>phenotype</th>\n",
" <th>idr0001-</th>\n",
" <th>idr0002-</th>\n",
" <th>idr0003-</th>\n",
" <th>idr0004-</th>\n",
" <th>idr0005-</th>\n",
" <th>idr0006-</th>\n",
" <th>idr0007-</th>\n",
" <th>idr0008-</th>\n",
" <th>idr0009-</th>\n",
" <th>idr0013-</th>\n",
" <th>Screens</th>\n",
" <th>Images</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>CMPO_0000398 ...</td>\n",
" <td>0</td>\n",
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" <td>10959</td>\n",
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" <td>3</td>\n",
" <td>12067</td>\n",
" </tr>\n",
" <tr>\n",
" <th>67</th>\n",
" <td>CMPO_0000077 ...</td>\n",
" <td>2788</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>3886</td>\n",
" </tr>\n",
" <tr>\n",
" <th>34</th>\n",
" <td>CMPO_0000140 ...</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>57</td>\n",
" <td>0</td>\n",
" <td>781</td>\n",
" <td>2</td>\n",
" <td>838</td>\n",
" </tr>\n",
" <tr>\n",
" <th>80</th>\n",
" <td>CMPO_0000118 ...</td>\n",
" <td>99</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>189</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" <td>288</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>CMPO_0000397 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>897</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>2320</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" <td>3217</td>\n",
" </tr>\n",
" <tr>\n",
" <th>81</th>\n",
" <td>CMPO_0000116 ...</td>\n",
" <td>12241</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>78</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" <td>12319</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CMPO_0000402 ...</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>630</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",
" <td>630</td>\n",
" </tr>\n",
" <tr>\n",
" <th>62</th>\n",
" <td>CMPO_0000277 ...</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>15</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" <td>15</td>\n",
" </tr>\n",
" <tr>\n",
" <th>68</th>\n",
" <td>CMPO_0000076 ...</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>753</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" <td>753</td>\n",
" </tr>\n",
" <tr>\n",
" <th>66</th>\n",
" <td>CMPO_0000372 ...</td>\n",
" <td>1427</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>0</td>\n",
" <td>1</td>\n",
" <td>1427</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" phenotype idr0001- idr0002- \\\n",
"11 CMPO_0000398 ... 0 0 \n",
"67 CMPO_0000077 ... 2788 0 \n",
"34 CMPO_0000140 ... 0 0 \n",
"80 CMPO_0000118 ... 99 0 \n",
"16 CMPO_0000397 ... 0 0 \n",
"81 CMPO_0000116 ... 12241 0 \n",
"0 CMPO_0000402 ... 0 0 \n",
"62 CMPO_0000277 ... 0 0 \n",
"68 CMPO_0000076 ... 0 0 \n",
"66 CMPO_0000372 ... 1427 0 \n",
"\n",
" idr0003- idr0004- idr0005- idr0006- idr0007- idr0008- idr0009- \\\n",
"11 10959 0 0 1024 84 0 0 \n",
"67 0 0 0 0 0 1098 0 \n",
"34 0 0 0 0 0 57 0 \n",
"80 0 0 0 0 0 189 0 \n",
"16 897 0 0 2320 0 0 0 \n",
"81 0 0 0 0 78 0 0 \n",
"0 630 0 0 0 0 0 0 \n",
"62 0 0 0 0 0 15 0 \n",
"68 0 0 0 0 0 753 0 \n",
"66 0 0 0 0 0 0 0 \n",
"\n",
" idr0013- Screens Images \n",
"11 0 3 12067 \n",
"67 0 2 3886 \n",
"34 781 2 838 \n",
"80 0 2 288 \n",
"16 0 2 3217 \n",
"81 0 2 12319 \n",
"0 0 1 630 \n",
"62 0 1 15 \n",
"68 0 1 753 \n",
"66 0 1 1427 "
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"phenotype.sort(\"Screens\", ascending=False)[0:10]"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"sirna = read_csv(\"../data/sirna.tsv\", delimiter=\"\\t\")"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <th>idr0009-</th>\n",
" <th>idr0013-</th>\n",
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" <th>Images</th>\n",
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" <td>21685 ...</td>\n",
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"</table>\n",
"</div>"
],
"text/plain": [
" sirna idr0001- idr0002- \\\n",
"0 228055 ... 0 0 \n",
"47409 143202 ... 0 0 \n",
"47411 216637 ... 0 0 \n",
"47412 216630 ... 0 0 \n",
"47413 10791 ... 0 0 \n",
"47414 10792 ... 0 0 \n",
"47415 216633 ... 0 0 \n",
"47416 246697 ... 0 0 \n",
"47418 21685 ... 0 0 \n",
"47419 144252 ... 0 0 \n",
"\n",
" idr0003- idr0004- idr0005- idr0006- idr0007- idr0008- idr0009- \\\n",
"0 0 0 0 0 0 0 9 \n",
"47409 0 0 0 0 0 0 6 \n",
"47411 0 0 0 0 0 0 9 \n",
"47412 0 0 0 0 0 0 9 \n",
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"47418 0 0 0 0 0 0 6 \n",
"47419 0 0 0 0 0 0 5 \n",
"\n",
" idr0013- Screens Images \n",
"0 3 2 12 \n",
"47409 4 2 10 \n",
"47411 3 2 12 \n",
"47412 3 2 12 \n",
"47413 5 2 12 \n",
"47414 4 2 10 \n",
"47415 3 2 9 \n",
"47416 3 2 9 \n",
"47418 3 2 9 \n",
"47419 3 2 8 "
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sirna.sort(\"Screens\", ascending=False)[0:10]"
]
}
],
"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"
}
},
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"nbformat_minor": 0
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