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ecwheele/Compare_editing_sites.ipynb

Created May 15, 2017 19:24
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Compare_editing_sites.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 61,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import pandas as pd\n",
"from matplotlib import pyplot as plt\n",
"import seaborn as sns\n",
"%matplotlib inline"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"directory = '/projects/ps-yeolab3/ecwheele/adar3_eimile_hundley/sailor_results/'\n",
"\n",
"samples = ['GSF860-Hundley-22_S1_R1_001','GSF860-Hundley-18_S5_R1_001','GSF860-Hundley-17_S4_R1_001',\n",
" 'GSF860-Hundley-16_S3_R1_001','GSF860-Hundley-14_S2_R1_001','GSF860-Hundley-13_S1_R1_001']"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"bed = \".combined.bed\""
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def load_df_and_make_id(filename):\n",
"\n",
" names = ['chrom','start','stop','name','score','strand']\n",
"\n",
" df = pd.read_table(filename, names = names)\n",
" df['id'] = df['chrom']+\":\"+df['start'].astype(str)+\"-\"+df['stop'].astype(str)+\"(\"+df['strand']+\")\"\n",
" df.set_index('id',inplace=True)\n",
" df_filt = df.loc[df['score'] > 0.95]\n",
" return df, df_filt"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"s13, s13_filt = load_df_and_make_id(directory+'GSF860-Hundley-13_S1_R1_001'+bed)\n",
"s14, s14_filt = load_df_and_make_id(directory+'GSF860-Hundley-14_S2_R1_001'+bed)\n",
"s16, s16_filt = load_df_and_make_id(directory+'GSF860-Hundley-16_S3_R1_001'+bed)\n",
"s17, s17_filt = load_df_and_make_id(directory+'GSF860-Hundley-17_S4_R1_001'+bed)\n",
"s18, s18_filt = load_df_and_make_id(directory+'GSF860-Hundley-18_S5_R1_001'+bed)\n",
"s22, s22_filt = load_df_and_make_id(directory+'GSF860-Hundley-22_S1_R1_001'+bed)"
]
},
{
"cell_type": "code",
"execution_count": 53,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"dfs = [s13_filt,s14_filt,s16_filt,s17_filt,s18_filt,s22_filt]\n",
"samples = ['s13','s14','s16','s17','s18','s22']"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/ecwheele/anaconda2/lib/python2.7/site-packages/ipykernel/__main__.py:2: SettingWithCopyWarning: \n",
"A value is trying to be set on a copy of a slice from a DataFrame.\n",
"Try using .loc[row_indexer,col_indexer] = value instead\n",
"\n",
"See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
" from ipykernel import kernelapp as app\n"
]
}
],
"source": [
"for i in dfs:\n",
" i['edit_fraction'] = i['name'].apply(lambda x:x.split(\"|\")[2])"
]
},
{
"cell_type": "code",
"execution_count": 91,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(36957, 6)\n",
"(1827, 6)\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>edit_fraction_s13</th>\n",
" <th>edit_fraction_s14</th>\n",
" <th>edit_fraction_s16</th>\n",
" <th>edit_fraction_s17</th>\n",
" <th>edit_fraction_s18</th>\n",
" <th>edit_fraction_s22</th>\n",
" </tr>\n",
" <tr>\n",
" <th>id</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" <tbody>\n",
" <tr>\n",
" <th>chr10:100152282-100152283(-)</th>\n",
" <td>0.333333333</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>chr10:100157193-100157194(-)</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.133333333</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:100173858-100173859(-)</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.2</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:100183505-100183506(-)</th>\n",
" <td>NaN</td>\n",
" <td>0.2</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:100185410-100185411(-)</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.055555556</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" edit_fraction_s13 edit_fraction_s14 \\\n",
"id \n",
"chr10:100152282-100152283(-) 0.333333333 NaN \n",
"chr10:100157193-100157194(-) NaN NaN \n",
"chr10:100173858-100173859(-) NaN NaN \n",
"chr10:100183505-100183506(-) NaN 0.2 \n",
"chr10:100185410-100185411(-) NaN NaN \n",
"\n",
" edit_fraction_s16 edit_fraction_s17 \\\n",
"id \n",
"chr10:100152282-100152283(-) NaN NaN \n",
"chr10:100157193-100157194(-) NaN NaN \n",
"chr10:100173858-100173859(-) 0.2 NaN \n",
"chr10:100183505-100183506(-) NaN NaN \n",
"chr10:100185410-100185411(-) NaN 0.055555556 \n",
"\n",
" edit_fraction_s18 edit_fraction_s22 \n",
"id \n",
"chr10:100152282-100152283(-) NaN NaN \n",
"chr10:100157193-100157194(-) NaN 0.133333333 \n",
"chr10:100173858-100173859(-) NaN NaN \n",
"chr10:100183505-100183506(-) NaN NaN \n",
"chr10:100185410-100185411(-) NaN NaN "
]
},
"execution_count": 91,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"filt_combined = pd.DataFrame()\n",
"\n",
"for i, name in zip(dfs, samples):\n",
" filt_combined = filt_combined.join(i['edit_fraction'], rsuffix = \"_\"+name, how=\"outer\")\n",
"\n",
"filt_combined.rename(columns = {\"edit_fraction\":\"edit_fraction_s13\"}, inplace=True)\n",
"print filt_combined.shape\n",
"filt_combined_common = filt_combined.dropna(axis=0)\n",
"print filt_combined_common.shape\n",
"filt_combined.head()\n"
]
},
{
"cell_type": "code",
"execution_count": 92,
"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>edit_fraction_s13</th>\n",
" <th>edit_fraction_s14</th>\n",
" <th>edit_fraction_s16</th>\n",
" <th>edit_fraction_s17</th>\n",
" <th>edit_fraction_s18</th>\n",
" <th>edit_fraction_s22</th>\n",
" </tr>\n",
" <tr>\n",
" <th>id</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>chr10:101992306-101992307(-)</th>\n",
" <td>0.8</td>\n",
" <td>0.381818182</td>\n",
" <td>0.604651163</td>\n",
" <td>0.529411765</td>\n",
" <td>0.52173913</td>\n",
" <td>0.515151515</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:101992313-101992314(-)</th>\n",
" <td>0.4</td>\n",
" <td>0.345454545</td>\n",
" <td>0.404761905</td>\n",
" <td>0.3125</td>\n",
" <td>0.47826087</td>\n",
" <td>0.441176471</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:12209751-12209752(-)</th>\n",
" <td>0.543307087</td>\n",
" <td>0.518518519</td>\n",
" <td>0.523734177</td>\n",
" <td>0.397905759</td>\n",
" <td>0.380645161</td>\n",
" <td>0.388446215</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:13239650-13239651(+)</th>\n",
" <td>0.434782609</td>\n",
" <td>0.485294118</td>\n",
" <td>0.296296296</td>\n",
" <td>0.166666667</td>\n",
" <td>0.52173913</td>\n",
" <td>0.454545455</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:13653652-13653653(+)</th>\n",
" <td>0.465116279</td>\n",
" <td>0.555555556</td>\n",
" <td>0.580645161</td>\n",
" <td>0.666666667</td>\n",
" <td>0.673076923</td>\n",
" <td>0.580246914</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" edit_fraction_s13 edit_fraction_s14 \\\n",
"id \n",
"chr10:101992306-101992307(-) 0.8 0.381818182 \n",
"chr10:101992313-101992314(-) 0.4 0.345454545 \n",
"chr10:12209751-12209752(-) 0.543307087 0.518518519 \n",
"chr10:13239650-13239651(+) 0.434782609 0.485294118 \n",
"chr10:13653652-13653653(+) 0.465116279 0.555555556 \n",
"\n",
" edit_fraction_s16 edit_fraction_s17 \\\n",
"id \n",
"chr10:101992306-101992307(-) 0.604651163 0.529411765 \n",
"chr10:101992313-101992314(-) 0.404761905 0.3125 \n",
"chr10:12209751-12209752(-) 0.523734177 0.397905759 \n",
"chr10:13239650-13239651(+) 0.296296296 0.166666667 \n",
"chr10:13653652-13653653(+) 0.580645161 0.666666667 \n",
"\n",
" edit_fraction_s18 edit_fraction_s22 \n",
"id \n",
"chr10:101992306-101992307(-) 0.52173913 0.515151515 \n",
"chr10:101992313-101992314(-) 0.47826087 0.441176471 \n",
"chr10:12209751-12209752(-) 0.380645161 0.388446215 \n",
"chr10:13239650-13239651(+) 0.52173913 0.454545455 \n",
"chr10:13653652-13653653(+) 0.673076923 0.580246914 "
]
},
"execution_count": 92,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"filt_combined_common.head()"
]
},
{
"cell_type": "code",
"execution_count": 96,
"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",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"Empty DataFrame\n",
"Columns: []\n",
"Index: []"
]
},
"execution_count": 96,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"filt_combined_common.head().corr()"
]
},
{
"cell_type": "code",
"execution_count": 94,
"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>edit_fraction_s13</th>\n",
" <th>edit_fraction_s14</th>\n",
" <th>edit_fraction_s16</th>\n",
" <th>edit_fraction_s17</th>\n",
" <th>edit_fraction_s18</th>\n",
" <th>edit_fraction_s22</th>\n",
" </tr>\n",
" <tr>\n",
" <th>id</th>\n",
" <th></th>\n",
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" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>chr10:101992306-101992307(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:101992313-101992314(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:12209751-12209752(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:13239650-13239651(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:13653652-13653653(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:13688570-13688571(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:22839627-22839628(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:24908685-24908686(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:25312688-25312689(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:27508757-27508758(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:29715865-29715866(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:29754608-29754609(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:29754643-29754644(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:3169138-3169139(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:3170742-3170743(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:3180315-3180316(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:33466518-33466519(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:33466842-33466843(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:33468013-33468014(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:3820786-3820787(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:38376743-38376744(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:47396575-47396576(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:49239506-49239507(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:5041397-5041398(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:52065889-52065890(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:5637027-5637028(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:5799612-5799613(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:73980018-73980019(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:74766317-74766318(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr10:75008730-75008731(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:70631386-70631387(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:70862676-70862677(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:74969863-74969864(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:75766837-75766838(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:75775234-75775235(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:75783936-75783937(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:79002060-79002061(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:79118660-79118661(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:79986056-79986057(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:79999782-79999783(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:86278877-86278878(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:91656962-91656963(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:94841501-94841502(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:96941576-96941577(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:97849089-97849090(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chr9:99252463-99252464(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:123047294-123047295(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:134156028-134156029(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:13734725-13734726(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:147134198-147134199(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:153061313-153061314(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:155252735-155252736(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:155252757-155252758(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:2824316-2824317(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:73166844-73166845(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:73166905-73166906(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:73417058-73417059(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:77083040-77083041(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:77083120-77083121(-)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" <tr>\n",
" <th>chrX:77387619-77387620(+)</th>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>1827 rows × 6 columns</p>\n",
"</div>"
],
"text/plain": [
" edit_fraction_s13 edit_fraction_s14 \\\n",
"id \n",
"chr10:101992306-101992307(-) False False \n",
"chr10:101992313-101992314(-) False False \n",
"chr10:12209751-12209752(-) False False \n",
"chr10:13239650-13239651(+) False False \n",
"chr10:13653652-13653653(+) False False \n",
"chr10:13688570-13688571(-) False False \n",
"chr10:22839627-22839628(-) False False \n",
"chr10:24908685-24908686(-) False False \n",
"chr10:25312688-25312689(+) False False \n",
"chr10:27508757-27508758(-) False False \n",
"chr10:29715865-29715866(+) False False \n",
"chr10:29754608-29754609(-) False False \n",
"chr10:29754643-29754644(-) False False \n",
"chr10:3169138-3169139(+) False False \n",
"chr10:3170742-3170743(+) False False \n",
"chr10:3180315-3180316(-) False False \n",
"chr10:33466518-33466519(-) False False \n",
"chr10:33466842-33466843(-) False False \n",
"chr10:33468013-33468014(-) False False \n",
"chr10:3820786-3820787(-) False False \n",
"chr10:38376743-38376744(-) False False \n",
"chr10:47396575-47396576(+) False False \n",
"chr10:49239506-49239507(-) False False \n",
"chr10:5041397-5041398(-) False False \n",
"chr10:52065889-52065890(-) False False \n",
"chr10:5637027-5637028(-) False False \n",
"chr10:5799612-5799613(+) False False \n",
"chr10:73980018-73980019(+) False False \n",
"chr10:74766317-74766318(-) False False \n",
"chr10:75008730-75008731(-) False False \n",
"... ... ... \n",
"chr9:70631386-70631387(-) False False \n",
"chr9:70862676-70862677(+) False False \n",
"chr9:74969863-74969864(-) False False \n",
"chr9:75766837-75766838(+) False False \n",
"chr9:75775234-75775235(+) False False \n",
"chr9:75783936-75783937(+) False False \n",
"chr9:79002060-79002061(-) False False \n",
"chr9:79118660-79118661(+) False False \n",
"chr9:79986056-79986057(+) False False \n",
"chr9:79999782-79999783(+) False False \n",
"chr9:86278877-86278878(-) False False \n",
"chr9:91656962-91656963(-) False False \n",
"chr9:94841501-94841502(-) False False \n",
"chr9:96941576-96941577(+) False False \n",
"chr9:97849089-97849090(+) False False \n",
"chr9:99252463-99252464(+) False False \n",
"chrX:123047294-123047295(+) False False \n",
"chrX:134156028-134156029(-) False False \n",
"chrX:13734725-13734726(-) False False \n",
"chrX:147134198-147134199(+) False False \n",
"chrX:153061313-153061314(+) False False \n",
"chrX:155252735-155252736(+) False False \n",
"chrX:155252757-155252758(+) False False \n",
"chrX:2824316-2824317(-) False False \n",
"chrX:73166844-73166845(+) False False \n",
"chrX:73166905-73166906(+) False False \n",
"chrX:73417058-73417059(-) False False \n",
"chrX:77083040-77083041(-) False False \n",
"chrX:77083120-77083121(-) False False \n",
"chrX:77387619-77387620(+) False False \n",
"\n",
" edit_fraction_s16 edit_fraction_s17 \\\n",
"id \n",
"chr10:101992306-101992307(-) False False \n",
"chr10:101992313-101992314(-) False False \n",
"chr10:12209751-12209752(-) False False \n",
"chr10:13239650-13239651(+) False False \n",
"chr10:13653652-13653653(+) False False \n",
"chr10:13688570-13688571(-) False False \n",
"chr10:22839627-22839628(-) False False \n",
"chr10:24908685-24908686(-) False False \n",
"chr10:25312688-25312689(+) False False \n",
"chr10:27508757-27508758(-) False False \n",
"chr10:29715865-29715866(+) False False \n",
"chr10:29754608-29754609(-) False False \n",
"chr10:29754643-29754644(-) False False \n",
"chr10:3169138-3169139(+) False False \n",
"chr10:3170742-3170743(+) False False \n",
"chr10:3180315-3180316(-) False False \n",
"chr10:33466518-33466519(-) False False \n",
"chr10:33466842-33466843(-) False False \n",
"chr10:33468013-33468014(-) False False \n",
"chr10:3820786-3820787(-) False False \n",
"chr10:38376743-38376744(-) False False \n",
"chr10:47396575-47396576(+) False False \n",
"chr10:49239506-49239507(-) False False \n",
"chr10:5041397-5041398(-) False False \n",
"chr10:52065889-52065890(-) False False \n",
"chr10:5637027-5637028(-) False False \n",
"chr10:5799612-5799613(+) False False \n",
"chr10:73980018-73980019(+) False False \n",
"chr10:74766317-74766318(-) False False \n",
"chr10:75008730-75008731(-) False False \n",
"... ... ... \n",
"chr9:70631386-70631387(-) False False \n",
"chr9:70862676-70862677(+) False False \n",
"chr9:74969863-74969864(-) False False \n",
"chr9:75766837-75766838(+) False False \n",
"chr9:75775234-75775235(+) False False \n",
"chr9:75783936-75783937(+) False False \n",
"chr9:79002060-79002061(-) False False \n",
"chr9:79118660-79118661(+) False False \n",
"chr9:79986056-79986057(+) False False \n",
"chr9:79999782-79999783(+) False False \n",
"chr9:86278877-86278878(-) False False \n",
"chr9:91656962-91656963(-) False False \n",
"chr9:94841501-94841502(-) False False \n",
"chr9:96941576-96941577(+) False False \n",
"chr9:97849089-97849090(+) False False \n",
"chr9:99252463-99252464(+) False False \n",
"chrX:123047294-123047295(+) False False \n",
"chrX:134156028-134156029(-) False False \n",
"chrX:13734725-13734726(-) False False \n",
"chrX:147134198-147134199(+) False False \n",
"chrX:153061313-153061314(+) False False \n",
"chrX:155252735-155252736(+) False False \n",
"chrX:155252757-155252758(+) False False \n",
"chrX:2824316-2824317(-) False False \n",
"chrX:73166844-73166845(+) False False \n",
"chrX:73166905-73166906(+) False False \n",
"chrX:73417058-73417059(-) False False \n",
"chrX:77083040-77083041(-) False False \n",
"chrX:77083120-77083121(-) False False \n",
"chrX:77387619-77387620(+) False False \n",
"\n",
" edit_fraction_s18 edit_fraction_s22 \n",
"id \n",
"chr10:101992306-101992307(-) False False \n",
"chr10:101992313-101992314(-) False False \n",
"chr10:12209751-12209752(-) False False \n",
"chr10:13239650-13239651(+) False False \n",
"chr10:13653652-13653653(+) False False \n",
"chr10:13688570-13688571(-) False False \n",
"chr10:22839627-22839628(-) False False \n",
"chr10:24908685-24908686(-) False False \n",
"chr10:25312688-25312689(+) False False \n",
"chr10:27508757-27508758(-) False False \n",
"chr10:29715865-29715866(+) False False \n",
"chr10:29754608-29754609(-) False False \n",
"chr10:29754643-29754644(-) False False \n",
"chr10:3169138-3169139(+) False False \n",
"chr10:3170742-3170743(+) False False \n",
"chr10:3180315-3180316(-) False False \n",
"chr10:33466518-33466519(-) False False \n",
"chr10:33466842-33466843(-) False False \n",
"chr10:33468013-33468014(-) False False \n",
"chr10:3820786-3820787(-) False False \n",
"chr10:38376743-38376744(-) False False \n",
"chr10:47396575-47396576(+) False False \n",
"chr10:49239506-49239507(-) False False \n",
"chr10:5041397-5041398(-) False False \n",
"chr10:52065889-52065890(-) False False \n",
"chr10:5637027-5637028(-) False False \n",
"chr10:5799612-5799613(+) False False \n",
"chr10:73980018-73980019(+) False False \n",
"chr10:74766317-74766318(-) False False \n",
"chr10:75008730-75008731(-) False False \n",
"... ... ... \n",
"chr9:70631386-70631387(-) False False \n",
"chr9:70862676-70862677(+) False False \n",
"chr9:74969863-74969864(-) False False \n",
"chr9:75766837-75766838(+) False False \n",
"chr9:75775234-75775235(+) False False \n",
"chr9:75783936-75783937(+) False False \n",
"chr9:79002060-79002061(-) False False \n",
"chr9:79118660-79118661(+) False False \n",
"chr9:79986056-79986057(+) False False \n",
"chr9:79999782-79999783(+) False False \n",
"chr9:86278877-86278878(-) False False \n",
"chr9:91656962-91656963(-) False False \n",
"chr9:94841501-94841502(-) False False \n",
"chr9:96941576-96941577(+) False False \n",
"chr9:97849089-97849090(+) False False \n",
"chr9:99252463-99252464(+) False False \n",
"chrX:123047294-123047295(+) False False \n",
"chrX:134156028-134156029(-) False False \n",
"chrX:13734725-13734726(-) False False \n",
"chrX:147134198-147134199(+) False False \n",
"chrX:153061313-153061314(+) False False \n",
"chrX:155252735-155252736(+) False False \n",
"chrX:155252757-155252758(+) False False \n",
"chrX:2824316-2824317(-) False False \n",
"chrX:73166844-73166845(+) False False \n",
"chrX:73166905-73166906(+) False False \n",
"chrX:73417058-73417059(-) False False \n",
"chrX:77083040-77083041(-) False False \n",
"chrX:77083120-77083121(-) False False \n",
"chrX:77387619-77387620(+) False False \n",
"\n",
"[1827 rows x 6 columns]"
]
},
"execution_count": 94,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"filt_combined_common.isnull()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"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": "2.7.12"
}
},
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"nbformat_minor": 0
}
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