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Phlya/Snipper_error.ipynb

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Snipper_error.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import cooler\n",
"from cooltools import snipping\n",
"import pandas as pd"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"exp = pd.read_csv('expected/Rhodes_Tir1+Aux_10000.expected.tsv', sep='\\t')\n",
"c = cooler.Cooler('coolers/Rhodes_Tir1+Aux.mm10.mapq_30.1000.mcool::resolutions/10000')"
]
},
{
"cell_type": "code",
"execution_count": 6,
"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>diag</th>\n",
" <th>n_valid</th>\n",
" <th>count.sum</th>\n",
" <th>balanced.sum</th>\n",
" <th>count.avg</th>\n",
" <th>balanced.avg</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>chr1</td>\n",
" <td>0</td>\n",
" <td>18543</td>\n",
" <td>1358299.0</td>\n",
" <td>1420.345584</td>\n",
" <td>73.251308</td>\n",
" <td>0.076597</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>chr1</td>\n",
" <td>1</td>\n",
" <td>18026</td>\n",
" <td>523355.0</td>\n",
" <td>519.968646</td>\n",
" <td>29.033341</td>\n",
" <td>0.028845</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>chr1</td>\n",
" <td>2</td>\n",
" <td>18019</td>\n",
" <td>276906.0</td>\n",
" <td>274.515863</td>\n",
" <td>15.367445</td>\n",
" <td>0.015235</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>chr1</td>\n",
" <td>3</td>\n",
" <td>17996</td>\n",
" <td>200786.0</td>\n",
" <td>198.583898</td>\n",
" <td>11.157257</td>\n",
" <td>0.011035</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>chr1</td>\n",
" <td>4</td>\n",
" <td>17990</td>\n",
" <td>161907.0</td>\n",
" <td>160.166109</td>\n",
" <td>8.999833</td>\n",
" <td>0.008903</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" chrom diag n_valid count.sum balanced.sum count.avg balanced.avg\n",
"0 chr1 0 18543 1358299.0 1420.345584 73.251308 0.076597\n",
"1 chr1 1 18026 523355.0 519.968646 29.033341 0.028845\n",
"2 chr1 2 18019 276906.0 274.515863 15.367445 0.015235\n",
"3 chr1 3 17996 200786.0 198.583898 11.157257 0.011035\n",
"4 chr1 4 17990 161907.0 160.166109 8.999833 0.008903"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exp.head()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"snipper = snipping.ExpectedSnipper(c, exp)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"ename": "ValueError",
"evalue": "Unknown sequence label: c",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/pandas/core/indexes/base.py\u001b[0m in \u001b[0;36mget_value\u001b[0;34m(self, series, key)\u001b[0m\n\u001b[1;32m 4409\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4410\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mlibindex\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_value_at\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4411\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mIndexError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.get_value_at\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.get_value_at\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/util.pxd\u001b[0m in \u001b[0;36mpandas._libs.util.get_value_at\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/util.pxd\u001b[0m in \u001b[0;36mpandas._libs.util.validate_indexer\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mTypeError\u001b[0m: 'str' object cannot be interpreted as an integer",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/Projects/cooler/cooler/util.py\u001b[0m in \u001b[0;36mparse_region\u001b[0;34m(reg, chromsizes)\u001b[0m\n\u001b[1;32m 166\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 167\u001b[0;31m \u001b[0mclen\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mchromsizes\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mchrom\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mchromsizes\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 168\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/pandas/core/series.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 870\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 871\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_value\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 872\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/pandas/core/indexes/base.py\u001b[0m in \u001b[0;36mget_value\u001b[0;34m(self, series, key)\u001b[0m\n\u001b[1;32m 4417\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4418\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0me1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4419\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/pandas/core/indexes/base.py\u001b[0m in \u001b[0;36mget_value\u001b[0;34m(self, series, key)\u001b[0m\n\u001b[1;32m 4403\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4404\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_value\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtz\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mseries\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"tz\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4405\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_value\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_value\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/hashtable_class_helper.pxi\u001b[0m in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mpandas/_libs/hashtable_class_helper.pxi\u001b[0m in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mKeyError\u001b[0m: 'c'",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-4-53f41e863751>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0msel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msnipper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mselect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'chr1'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'chr1'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/cooltools/snipping.py\u001b[0m in \u001b[0;36mselect\u001b[0;34m(self, region1, region2)\u001b[0m\n\u001b[1;32m 451\u001b[0m \u001b[0mregion1\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mregion2\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 452\u001b[0m ), \"ExpectedSnipper is implemented for cis contacts only.\"\n\u001b[0;32m--> 453\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moffsets\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mregion1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moffset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion1\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moffset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion1\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 454\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moffsets\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mregion2\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moffset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion2\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moffset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion2\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 455\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mm\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdiff\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextent\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Projects/cooler/cooler/api.py\u001b[0m in \u001b[0;36moffset\u001b[0;34m(self, region)\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0mgrp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroot\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 185\u001b[0m return region_to_offset(\n\u001b[0;32m--> 186\u001b[0;31m \u001b[0mgrp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_chromids\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparse_region\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_chromsizes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 187\u001b[0m )\n\u001b[1;32m 188\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Projects/cooler/cooler/util.py\u001b[0m in \u001b[0;36mparse_region\u001b[0;34m(reg, chromsizes)\u001b[0m\n\u001b[1;32m 167\u001b[0m \u001b[0mclen\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mchromsizes\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mchrom\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mchromsizes\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 168\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 169\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Unknown sequence label: {}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mchrom\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 170\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 171\u001b[0m \u001b[0mstart\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m0\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mstart\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mstart\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: Unknown sequence label: c"
]
}
],
"source": [
"sel = snipper.select('chr1', 'chr1')"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"('chr1', None, None)\n"
]
},
{
"ename": "KeyError",
"evalue": "('chr1', None, None)",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-5-51d2ef93c7c7>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mregion\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcooler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mutil\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparse_region_string\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'chr1'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0msel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msnipper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mselect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mregion\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mregion\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/cooltools/snipping.py\u001b[0m in \u001b[0;36mselect\u001b[0;34m(self, region1, region2)\u001b[0m\n\u001b[1;32m 457\u001b[0m \u001b[0mgr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexpected\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgroupby\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mregions_columns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 458\u001b[0m self._expected = LazyToeplitz( \n\u001b[0;32m--> 459\u001b[0;31m gr.get_group(tuple(region1))[\n\u001b[0m\u001b[1;32m 460\u001b[0m \u001b[0;34m\"balanced.avg\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 461\u001b[0m ]\n",
"\u001b[0;32m~/miniconda/envs/hic/lib/python3.7/site-packages/pandas/core/groupby/groupby.py\u001b[0m in \u001b[0;36mget_group\u001b[0;34m(self, name, obj)\u001b[0m\n\u001b[1;32m 684\u001b[0m \u001b[0minds\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_index\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 685\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 686\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 687\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 688\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_take_with_is_copy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minds\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mKeyError\u001b[0m: ('chr1', None, None)"
]
}
],
"source": [
"region = cooler.util.parse_region_string('chr1')\n",
"print(region)\n",
"sel = snipper.select(region, region)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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