mergeBedPE.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:56:56.502584",
     "start_time": "2016-05-25T10:56:56.500157"
    },
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# needs to have a 7th column: loopID (easily done with awk '{print $0\"\\t\"NR}')\n",
    "inbedpe = '5k10k25k.bedpe.gz'\n",
    "outbedpe = '5k10k25k_merged.bedpe'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:56:59.398118",
     "start_time": "2016-05-25T10:56:59.347170"
    },
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'\\nwith open(inbedpe, \\'rb\\') as f:\\n    for line in f: \\n        fields = line.rstrip().split(\"\\t\")   \\n        bedpe[fields[6]] = fields[0:6]\\n        bedpe[fields[6]].append(\\'\\n \\')\\n'"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "bedpe = dict()\n",
    "\n",
    "import gzip\n",
    "with gzip.open(inbedpe, 'rb') as f:\n",
    "    for line in f: \n",
    "        fields = line.rstrip().split(\"\\t\")   \n",
    "        bedpe[fields[6]] = fields[0:6]\n",
    "        bedpe[fields[6]].append('\\n ')\n",
    "    \n",
    "'''\n",
    "with open(inbedpe, 'rb') as f:\n",
    "    for line in f: \n",
    "        fields = line.rstrip().split(\"\\t\")   \n",
    "        bedpe[fields[6]] = fields[0:6]\n",
    "        bedpe[fields[6]].append('\\n ')\n",
    "'''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:57:47.158758",
     "start_time": "2016-05-25T10:57:47.027387"
    },
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import subprocess\n",
    "\n",
    "subprocess.call(\"zcat \" + inbedpe + \" | cut -f 1,2,3,7 | bedtools sort | bedtools merge -d 10 -c 4 -o distinct > /tmp/startMerged.bed\", shell = True)\n",
    "subprocess.call(\"zcat \" + inbedpe + \" | cut -f 4,5,6,7 |  bedtools sort | bedtools merge -d 10 -c 4 -o distinct > /tmp/stopMerged.bed\", shell = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:57:54.642116",
     "start_time": "2016-05-25T10:57:54.598291"
    },
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "Alist = list()\n",
    "Blist = list()\n",
    "\n",
    "A = open('/tmp/startMerged.bed', 'r')\n",
    "for line in A:\n",
    "    fields = line.rstrip().split(\"\\t\")\n",
    "    IDs = fields[3].split(',')\n",
    "    IDs = map(int, IDs)\n",
    "    IDs = set(IDs)\n",
    "    Alist.append(IDs)\n",
    "    \n",
    "B = open('/tmp/stopMerged.bed', 'r')\n",
    "for line in B:\n",
    "    fields = line.rstrip().split(\"\\t\")\n",
    "    IDs = fields[3].split(',')\n",
    "    IDs = map(int, IDs)\n",
    "    IDs = set(IDs)\n",
    "    Blist.append(IDs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:57:57.538742",
     "start_time": "2016-05-25T10:57:57.503401"
    },
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "Aset = map(set, Alist)\n",
    "Bset = map(set, Blist)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:58:09.622789",
     "start_time": "2016-05-25T10:57:59.241587"
    },
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "MergableList = list()\n",
    "for i in Aset:\n",
    "    for j in Bset:\n",
    "        O = i.intersection(j)\n",
    "        if len(O) > 1:\n",
    "            MergableList.append(O)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:58:09.626137",
     "start_time": "2016-05-25T10:58:09.623701"
    },
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "MergableList.sort(key=len, reverse=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T10:58:11.676314",
     "start_time": "2016-05-25T10:58:11.528476"
    },
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{1940, 1942, 1960, 2014, 2020, 2028, 2034, 2093, 2151, 2183},\n",
       " {10675, 10739, 10812, 10865, 10946, 10967, 10979, 10983, 10989, 10990},\n",
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       " {229, 267, 275, 349, 355, 421, 495, 510},\n",
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       " {3387, 3467, 3475, 3579, 3596, 3599, 3618, 3640},\n",
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       " {11828, 11903, 11948, 11963, 11977, 11996, 11997, 12003},\n",
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       " {1952, 2091, 2148, 2163, 2240, 2258, 2270},\n",
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       " {1911, 1935, 1945, 2004, 2030, 2057},\n",
       " {1815, 2007, 2099, 2262, 2263, 2288},\n",
       " {2038, 2164, 2190, 2228, 2278, 2313},\n",
       " {1864, 1920, 2153, 2225, 2234, 2275},\n",
       " {1939, 2019, 2077, 2084, 2103, 2145},\n",
       " {2015, 2046, 2124, 2207, 2253, 2267},\n",
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       " {12621, 12660, 12675, 12752, 12760, 12809},\n",
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       " {13423, 13524, 13576, 13716, 13766, 13820},\n",
       " {13408, 13470, 13485, 13674, 13675, 13722},\n",
       " {14417, 14452, 14454, 14456, 14500, 14513},\n",
       " {14365, 14407, 14424, 14461, 14469, 14556},\n",
       " {14259, 14369, 14437, 14446, 14483, 14496},\n",
       " {14492, 14497, 14543, 14586, 14606, 14617},\n",
       " {14101, 14102, 14103, 14273, 14275, 14323},\n",
       " {14986, 15029, 15082, 15093, 15118, 15153},\n",
       " {14912, 14949, 14957, 14968, 14979, 15127},\n",
       " {7654, 7660, 7670, 7684, 7699, 7702},\n",
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       " {5486, 5601, 5716, 6167, 6168},\n",
       " {153, 182, 203, 360, 377},\n",
       " {431, 453, 528, 537, 575},\n",
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       " {918, 991, 1128, 1129, 1235},\n",
       " {1280, 1310, 1311, 1342, 1358},\n",
       " {1088, 1344, 1356, 1423, 1450},\n",
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       " {1121, 1189, 1254, 1263, 1402},\n",
       " {2095, 2102, 2189, 2206, 2294},\n",
       " {2191, 2274, 2303, 2310, 2339},\n",
       " {1934, 2056, 2122, 2154, 2219},\n",
       " {2725, 2726, 2765, 2767, 2779},\n",
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       " {2578, 2579, 2627, 2640, 2693},\n",
       " {3105, 3108, 3137, 3155, 3184},\n",
       " {3688, 3690, 3778, 3780, 3804},\n",
       " {3516, 3533, 3570, 3571, 3660},\n",
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       " {3487, 3489, 3511, 3535, 3634},\n",
       " {4115, 4143, 4169, 4176, 4181},\n",
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       " {9703, 9855, 9905, 9928, 10032},\n",
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       " {14079, 14105, 14149, 14171, 14182},\n",
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       " {7501, 7510, 7532, 7548, 7567},\n",
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       " {6150, 6314, 6354, 6368},\n",
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       " {5638, 5947, 6112, 6152},\n",
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       " {445, 517, 612, 616},\n",
       " {1201, 1284, 1300, 1332},\n",
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       " {1074, 1122, 1196, 1309},\n",
       " {1057, 1070, 1087, 1153},\n",
       " {1230, 1314, 1329, 1392},\n",
       " {1333, 1335, 1353, 1407},\n",
       " {1013, 1148, 1203, 1278},\n",
       " {930, 974, 1015, 1040},\n",
       " {1053, 1177, 1192, 1234},\n",
       " {1237, 1408, 1456, 1472},\n",
       " {1075, 1158, 1181, 1249},\n",
       " {1267, 1312, 1319, 1325},\n",
       " {779, 997, 1009, 1296},\n",
       " {1989, 2109, 2137, 2200},\n",
       " {2118, 2160, 2284, 2336},\n",
       " {1881, 2182, 2349, 2350},\n",
       " {1823, 1890, 2027, 2059},\n",
       " {1946, 1948, 2013, 2083},\n",
       " {1877, 1938, 1970, 1985},\n",
       " {1840, 1888, 2089, 2179},\n",
       " {1953, 1984, 2022, 2193},\n",
       " {2347, 2352, 2354, 2356},\n",
       " {2114, 2139, 2260, 2273},\n",
       " {1724, 1901, 2065, 2111},\n",
       " {1875, 1876, 1924, 2123},\n",
       " {2058, 2298, 2309, 2331},\n",
       " {1808, 2001, 2008, 2227},\n",
       " {2477, 2553, 2567, 2665},\n",
       " {2588, 2589, 2619, 2755},\n",
       " {2609, 2615, 2639, 2666},\n",
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       " {2844, 2858, 2882, 2920},\n",
       " {2981, 3025, 3091, 3121},\n",
       " {3580, 3606, 3696, 3755},\n",
       " {3565, 3679, 3721, 3730},\n",
       " {3617, 3681, 3710, 3767},\n",
       " {3816, 3819, 3822, 3823},\n",
       " {3682, 3692, 3701, 3708},\n",
       " {3652, 3680, 3687, 3762},\n",
       " {3543, 3591, 3643, 3666},\n",
       " {3980, 3997, 3999, 4098},\n",
       " {4062, 4110, 4135, 4138},\n",
       " {4004, 4045, 4050, 4123},\n",
       " {4051, 4100, 4109, 4113},\n",
       " {3956, 4006, 4013, 4108},\n",
       " {4149, 4158, 4162, 4163},\n",
       " {4024, 4043, 4049, 4068},\n",
       " {3916, 3941, 3989, 4018},\n",
       " {3971, 3974, 3993, 4069},\n",
       " {3924, 3932, 3936, 3976},\n",
       " {3998, 4065, 4104, 4137},\n",
       " {4591, 4616, 4646, 4647},\n",
       " {4588, 4613, 4621, 4643},\n",
       " {4450, 4459, 4473, 4508},\n",
       " {4283, 4299, 4320, 4337},\n",
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       " {8582, 8702, 8735, 8890},\n",
       " {8123, 8153, 8289, 8404},\n",
       " {8545, 8549, 8740, 8756},\n",
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       " {6825, 6830, 6842, 6845},\n",
       " {6784, 6798, 6841, 6849},\n",
       " {6644, 6727, 6801, 6843},\n",
       " {6998, 7001, 7003, 7015},\n",
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       " {9622, 9670, 9787, 9922},\n",
       " {9548, 9774, 9785, 9907},\n",
       " {9781, 9826, 9863, 9962},\n",
       " {9733, 9972, 9984, 9996},\n",
       " {9835, 9870, 9873, 9909},\n",
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       " {12893, 12902, 12958},\n",
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       " {12255, 12356, 12358},\n",
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       " {12603, 12754, 12792},\n",
       " {12674, 12714, 12770},\n",
       " {12390, 12565, 12639},\n",
       " {12352, 12424, 12537},\n",
       " {12683, 12712, 12868},\n",
       " {12448, 12854, 12910},\n",
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       " {13506, 13666, 13676},\n",
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       " {13724, 13845, 13886},\n",
       " {13770, 13785, 13871},\n",
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       " {14028, 14058, 14136},\n",
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       " {14961, 15083, 15096},\n",
       " {15000, 15055, 15115},\n",
       " {14870, 14897, 14910},\n",
       " {14774, 14776, 14849},\n",
       " {15076, 15087, 15136},\n",
       " {14848, 14920, 14927},\n",
       " {15117, 15144, 15152},\n",
       " {14644, 14645, 14736},\n",
       " {14948, 15030, 15062},\n",
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       " {14859, 14916, 14930},\n",
       " {14955, 14977, 15011},\n",
       " {14971, 15044, 15098},\n",
       " {14934, 15023, 15071},\n",
       " {15015, 15043, 15045},\n",
       " {15036, 15097, 15121},\n",
       " {14786, 14800, 14808},\n",
       " {7191, 7256, 7607},\n",
       " {7369, 7416, 7587},\n",
       " {7518, 7542, 7545},\n",
       " {7698, 7700, 7701},\n",
       " {7496, 7506, 7507},\n",
       " {7305, 7322, 7402},\n",
       " {7648, 7689, 7696},\n",
       " {7357, 7428, 7438},\n",
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       " {7449, 7505, 7516},\n",
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       " {7350, 7443, 7553},\n",
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       " {7409, 7411, 7535},\n",
       " {7465, 7467, 7489},\n",
       " {7519, 7570, 7583},\n",
       " {7641, 7663, 7671},\n",
       " {5930, 5989},\n",
       " {5733, 6452},\n",
       " {6312, 6362},\n",
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       " {6081, 6201},\n",
       " {5850, 6008},\n",
       " {5636, 5687},\n",
       " {5262, 6023},\n",
       " {5728, 6097},\n",
       " {5899, 6058},\n",
       " {5685, 5699},\n",
       " {5948, 6056},\n",
       " {6054, 6063},\n",
       " {5884, 6327},\n",
       " {6253, 6285},\n",
       " {6303, 6383},\n",
       " {5608, 5622},\n",
       " {5882, 5895},\n",
       " {6138, 6229},\n",
       " {5742, 5910},\n",
       " {5956, 6336},\n",
       " {6034, 6300},\n",
       " {6431, 6524},\n",
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       " {5380, 5467},\n",
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       " {5471, 5501},\n",
       " {5881, 6060},\n",
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       " {5757, 5993},\n",
       " {6527, 6540},\n",
       " {5539, 5984},\n",
       " {5694, 5790},\n",
       " {5722, 5921},\n",
       " {5525, 5554},\n",
       " {6145, 6272},\n",
       " {5832, 5919},\n",
       " {6190, 6375},\n",
       " {5440, 5774},\n",
       " {5842, 5942},\n",
       " {6074, 6142},\n",
       " {5365, 5406},\n",
       " {6029, 6226},\n",
       " {5279, 5303},\n",
       " {6250, 6277},\n",
       " {5718, 5798},\n",
       " {6073, 6160},\n",
       " {5588, 5602},\n",
       " {5829, 6001},\n",
       " {5325, 5343},\n",
       " {5972, 6308},\n",
       " {5828, 6051},\n",
       " {6038, 6195},\n",
       " {6209, 6348},\n",
       " {6208, 6239},\n",
       " ...]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "MergableList"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T11:08:41.558698",
     "start_time": "2016-05-25T11:08:41.428142"
    },
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from numpy import mean\n",
    "OUT = open(outbedpe, 'w')\n",
    "OUT.write('\\t'.join(['CHR1', 'X1', 'X2','CHR2','Y1','Y2','\\n']))\n",
    "for e, SET in enumerate(MergableList):\n",
    "    if e > 10: \n",
    "        exit\n",
    "    #lowestX1 = 0\n",
    "    #higestY2 = 0\n",
    "    #lowestX2 = 0\n",
    "    #higestY1 = 0\n",
    "    c = 'a'\n",
    "    X1  = list()\n",
    "    X2  = list()\n",
    "    Y1  = list()\n",
    "    Y2  = list()\n",
    "    for E, ID in enumerate(SET):\n",
    "        ID = str(ID)\n",
    "        c = bedpe[ID][0]\n",
    "        X1.append(int(bedpe[ID][1]))\n",
    "        Y1.append(int(bedpe[ID][4]))\n",
    "        X2.append(int(bedpe[ID][2]))\n",
    "        Y2.append(int(bedpe[ID][5]))\n",
    "    OUT.write('\\t'.join(     map(str,[c, int(mean(X1)), int(mean(X2)),c,int(mean(Y1)),int(mean(Y2)),'\\n'])))    \n",
    "    # \n",
    "    #    if E == 0:\n",
    "    #        c = bedpe[ID][0]\n",
    "    #        lowestX1 = int(bedpe[ID][1])\n",
    "    #        lowestY1 = int(bedpe[ID][4])\n",
    "    #        higestX2 = int(bedpe[ID][2] )\n",
    "    #        higestY2 = int(bedpe[ID][5] )\n",
    "    #    else:\n",
    "    #        if int(bedpe[ID][1]) < lowestX1:\n",
    "    #            lowestX1 = int(bedpe[ID][1])\n",
    "    #        if int(bedpe[ID][5]) > higestY2:\n",
    "    #            higestY2 = int(bedpe[ID][5] )\n",
    "    #        if int(bedpe[ID][1]) < lowestX2:\n",
    "    #            lowestX2 = int(bedpe[ID][2])\n",
    "    #        if int(bedpe[ID][4]) > higestY1:\n",
    "    #            higestY1 = int(bedpe[ID][4] )\n",
    "    #OUT.write('\\t'.join(     map(str,[c, lowestX1, higestX2,c,lowestY1,higestY2,'\\n'])))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T11:08:43.767297",
     "start_time": "2016-05-25T11:08:43.743237"
    },
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "for ID in set(bedpe.keys()).symmetric_difference(set(map(str,[item for sublist in MergableList for item in sublist]))):\n",
    "    OUT.write('\\t'.join(bedpe[ID]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2016-05-25T11:08:45.619711",
     "start_time": "2016-05-25T11:08:45.617912"
    },
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "OUT.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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