BENG469_python_practice.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "f3d0265c-a487-44f8-83e3-6a977dd0182e",
   "metadata": {},
   "source": [
    "## 1. Iterate each line of the provided ATAC_meta.csv file (except the header line), write the first number of each line (i.e., the 2nd column/the “total” column) into a list."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "4cb86106-339d-4896-9ce5-d099d658ff2c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'barcode,total,duplicate,chimeric,unmapped,lowmapq,mitochondrial,nonprimary,passed_filters,is__cell_barcode,excluded_reason,TSS_fragments,DNase_sensitive_region_fragments,enhancer_region_fragments,promoter_region_fragments,on_target_fragments,blacklist_region_fragments,peak_region_fragments,peak_region_cutsites\\n'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "input_file=open('ATAC_meta.csv', 'r')\n",
    "input_file.readline()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "7f46cf6f-e7e7-4d5d-bc7a-3a17d5f7460d",
   "metadata": {},
   "outputs": [],
   "source": [
    "our_list=[]\n",
    "for line in input_file:\n",
    "    line=line.strip().split(',')\n",
    "    total=int(line[1])\n",
    "    our_list.append(total)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "2ab98b83-7dec-473a-82cc-0fffdd205e2b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[485,\n",
       " 4476,\n",
       " 6445,\n",
       " 6341,\n",
       " 38717,\n",
       " 8021,\n",
       " 3864,\n",
       " 20704,\n",
       " 5676,\n",
       " 5687,\n",
       " 4093,\n",
       " 6107,\n",
       " 5471,\n",
       " 7715,\n",
       " 4067,\n",
       " 8187,\n",
       " 3884,\n",
       " 7661,\n",
       " 4510,\n",
       " 2370,\n",
       " 4814,\n",
       " 664,\n",
       " 4187,\n",
       " 13445,\n",
       " 5329,\n",
       " 5786,\n",
       " 6720,\n",
       " 5858,\n",
       " 6620,\n",
       " 12014,\n",
       " 6198,\n",
       " 7287,\n",
       " 32407,\n",
       " 6581,\n",
       " 6957,\n",
       " 7773,\n",
       " 7341,\n",
       " 6941,\n",
       " 7268,\n",
       " 10538,\n",
       " 8985,\n",
       " 9661,\n",
       " 7899,\n",
       " 12518,\n",
       " 9411,\n",
       " 5567,\n",
       " 3582,\n",
       " 6955,\n",
       " 2954,\n",
       " 34935,\n",
       " 1973,\n",
       " 6933,\n",
       " 7921,\n",
       " 6972,\n",
       " 26895,\n",
       " 8712,\n",
       " 9601,\n",
       " 9323,\n",
       " 11157,\n",
       " 8572,\n",
       " 4687,\n",
       " 5784,\n",
       " 6419,\n",
       " 9467,\n",
       " 3831,\n",
       " 5880,\n",
       " 3460,\n",
       " 2454,\n",
       " 2914,\n",
       " 2254,\n",
       " 3958,\n",
       " 681,\n",
       " 4896,\n",
       " 11576,\n",
       " 2261,\n",
       " 6294,\n",
       " 4059,\n",
       " 3785,\n",
       " 4652,\n",
       " 5340,\n",
       " 3311,\n",
       " 4129,\n",
       " 5817,\n",
       " 4133,\n",
       " 3765,\n",
       " 6968,\n",
       " 5548,\n",
       " 4821,\n",
       " 6430,\n",
       " 6579,\n",
       " 6002,\n",
       " 3689,\n",
       " 4847,\n",
       " 6996,\n",
       " 12772,\n",
       " 2782,\n",
       " 6289,\n",
       " 4807,\n",
       " 2650,\n",
       " 27427,\n",
       " 1732,\n",
       " 6974,\n",
       " 6657,\n",
       " 9752,\n",
       " 27416,\n",
       " 20564,\n",
       " 12313,\n",
       " 8572,\n",
       " 13700,\n",
       " 17883,\n",
       " 4772,\n",
       " 6369,\n",
       " 4218,\n",
       " 4313,\n",
       " 3101,\n",
       " 7161,\n",
       " 2992,\n",
       " 4230,\n",
       " 3808,\n",
       " 5992,\n",
       " 4130,\n",
       " 831,\n",
       " 5855,\n",
       " 8034,\n",
       " 4545,\n",
       " 7141,\n",
       " 2706,\n",
       " 4172,\n",
       " 3537,\n",
       " 4717,\n",
       " 2956,\n",
       " 5091,\n",
       " 5292,\n",
       " 3529,\n",
       " 3831,\n",
       " 3477,\n",
       " 4478,\n",
       " 7461,\n",
       " 6122,\n",
       " 3881,\n",
       " 11135,\n",
       " 6310,\n",
       " 4990,\n",
       " 4162,\n",
       " 4412,\n",
       " 3209,\n",
       " 8355,\n",
       " 3690,\n",
       " 1714,\n",
       " 16140,\n",
       " 5403,\n",
       " 10603,\n",
       " 8564,\n",
       " 11497,\n",
       " 43789,\n",
       " 25325,\n",
       " 16911,\n",
       " 8576,\n",
       " 21891,\n",
       " 17245,\n",
       " 5368,\n",
       " 9390,\n",
       " 8161,\n",
       " 6231,\n",
       " 4952,\n",
       " 8301,\n",
       " 5259,\n",
       " 4312,\n",
       " 3189,\n",
       " 4712,\n",
       " 3374,\n",
       " 762,\n",
       " 5274,\n",
       " 17444,\n",
       " 4284,\n",
       " 4897,\n",
       " 3953,\n",
       " 6048,\n",
       " 7116,\n",
       " 8251,\n",
       " 4319,\n",
       " 5430,\n",
       " 5980,\n",
       " 3827,\n",
       " 5205,\n",
       " 5811,\n",
       " 4272,\n",
       " 7609,\n",
       " 8382,\n",
       " 5258,\n",
       " 9554,\n",
       " 6312,\n",
       " 2953,\n",
       " 7091,\n",
       " 4709,\n",
       " 5801,\n",
       " 4464,\n",
       " 3375,\n",
       " 2038,\n",
       " 20018,\n",
       " 2349,\n",
       " 12610,\n",
       " 12916,\n",
       " 12527,\n",
       " 100876,\n",
       " 15259,\n",
       " 11836,\n",
       " 57089,\n",
       " 12536,\n",
       " 16131,\n",
       " 11658,\n",
       " 16183,\n",
       " 18549,\n",
       " 22956,\n",
       " 13878,\n",
       " 19842,\n",
       " 9977,\n",
       " 12162,\n",
       " 12049,\n",
       " 12163,\n",
       " 10061,\n",
       " 1741,\n",
       " 12348,\n",
       " 36955,\n",
       " 11102,\n",
       " 14585,\n",
       " 20272,\n",
       " 12466,\n",
       " 13008,\n",
       " 72884,\n",
       " 18792,\n",
       " 13975,\n",
       " 28527,\n",
       " 19100,\n",
       " 21669,\n",
       " 18561,\n",
       " 19587,\n",
       " 17429,\n",
       " 21173,\n",
       " 22902,\n",
       " 41686,\n",
       " 19935,\n",
       " 17171,\n",
       " 23638,\n",
       " 22251,\n",
       " 15934,\n",
       " 8748,\n",
       " 16853,\n",
       " 8011,\n",
       " 47148,\n",
       " 1373,\n",
       " 4964,\n",
       " 3913,\n",
       " 5374,\n",
       " 32826,\n",
       " 8979,\n",
       " 11241,\n",
       " 11958,\n",
       " 10469,\n",
       " 6416,\n",
       " 4381,\n",
       " 7926,\n",
       " 5916,\n",
       " 5435,\n",
       " 5481,\n",
       " 5437,\n",
       " 3912,\n",
       " 4830,\n",
       " 4808,\n",
       " 3594,\n",
       " 3669,\n",
       " 839,\n",
       " 5491,\n",
       " 7514,\n",
       " 5843,\n",
       " 6834,\n",
       " 3659,\n",
       " 5902,\n",
       " 4453,\n",
       " 4791,\n",
       " 4382,\n",
       " 3648,\n",
       " 4526,\n",
       " 4539,\n",
       " 6082,\n",
       " 5458,\n",
       " 4673,\n",
       " 5284,\n",
       " 10008,\n",
       " 5982,\n",
       " 8083,\n",
       " 3057,\n",
       " 2603,\n",
       " 5130,\n",
       " 12120,\n",
       " 4431,\n",
       " 5002,\n",
       " 4440,\n",
       " 1419,\n",
       " 29201,\n",
       " 1729,\n",
       " 1868,\n",
       " 6059,\n",
       " 5396,\n",
       " 24688,\n",
       " 2935,\n",
       " 3917,\n",
       " 8994,\n",
       " 5142,\n",
       " 5891,\n",
       " 4158,\n",
       " 5151,\n",
       " 6006,\n",
       " 6003,\n",
       " 3382,\n",
       " 3061,\n",
       " 2675,\n",
       " 4743,\n",
       " 3776,\n",
       " 1687,\n",
       " 3377,\n",
       " 577,\n",
       " 3999,\n",
       " 10778,\n",
       " 3163,\n",
       " 5779,\n",
       " 3914,\n",
       " 2570,\n",
       " 2381,\n",
       " 3211,\n",
       " 4077,\n",
       " 3452,\n",
       " 3631,\n",
       " 3000,\n",
       " 3096,\n",
       " 5478,\n",
       " 4574,\n",
       " 2733,\n",
       " 3368,\n",
       " 3380,\n",
       " 5641,\n",
       " 2537,\n",
       " 2952,\n",
       " 3706,\n",
       " 5097,\n",
       " 3581,\n",
       " 3790,\n",
       " 3161,\n",
       " 1411,\n",
       " 31966,\n",
       " 1577,\n",
       " 3923,\n",
       " 2946,\n",
       " 5613,\n",
       " 28112,\n",
       " 12584,\n",
       " 17270,\n",
       " 4137,\n",
       " 16857,\n",
       " 11987,\n",
       " 3627,\n",
       " 5813,\n",
       " 4176,\n",
       " 8946,\n",
       " 7332,\n",
       " 5076,\n",
       " 2392,\n",
       " 5283,\n",
       " 4289,\n",
       " 1995,\n",
       " 4493,\n",
       " 668,\n",
       " 10132,\n",
       " 10693,\n",
       " 4516,\n",
       " 4715,\n",
       " 2271,\n",
       " 7329,\n",
       " 9476,\n",
       " 14014,\n",
       " 3950,\n",
       " 4460,\n",
       " 9710,\n",
       " 5231,\n",
       " 7812,\n",
       " 7918,\n",
       " 5581,\n",
       " 7273,\n",
       " 4808,\n",
       " 5616,\n",
       " 3773,\n",
       " 6198,\n",
       " 3368,\n",
       " 3887,\n",
       " 3146,\n",
       " 2885,\n",
       " 4912,\n",
       " 4142,\n",
       " 1757,\n",
       " 27183,\n",
       " 1669,\n",
       " 1925,\n",
       " 15950,\n",
       " 18499,\n",
       " 25750,\n",
       " 11308,\n",
       " 2254,\n",
       " 12792,\n",
       " 2842,\n",
       " 5342,\n",
       " 3204,\n",
       " 5304,\n",
       " 4829,\n",
       " 5445,\n",
       " 3420,\n",
       " 5031,\n",
       " 3992,\n",
       " 5449,\n",
       " 3651,\n",
       " 1120,\n",
       " 4980,\n",
       " 507,\n",
       " 5251,\n",
       " 7411,\n",
       " 4429,\n",
       " 5049,\n",
       " 3885,\n",
       " 2525,\n",
       " 2717,\n",
       " 3553,\n",
       " 2544,\n",
       " 3828,\n",
       " 3639,\n",
       " 2725,\n",
       " 2616,\n",
       " 5757,\n",
       " 3186,\n",
       " 3235,\n",
       " 3527,\n",
       " 4077,\n",
       " 3155,\n",
       " 3468,\n",
       " 1783,\n",
       " 2904,\n",
       " 2058,\n",
       " 2708,\n",
       " 4553,\n",
       " 3591,\n",
       " 2372,\n",
       " 39858,\n",
       " 1163,\n",
       " 1820,\n",
       " 5114,\n",
       " 19987,\n",
       " 29757,\n",
       " 28702,\n",
       " 12523,\n",
       " 6533,\n",
       " 1890,\n",
       " 3828,\n",
       " 3330,\n",
       " 5039,\n",
       " 6305,\n",
       " 4102,\n",
       " 3008,\n",
       " 6085,\n",
       " 5924,\n",
       " 7294,\n",
       " 4913,\n",
       " 1926,\n",
       " 3178,\n",
       " 619,\n",
       " 6325,\n",
       " 9296,\n",
       " 5165,\n",
       " 5427,\n",
       " 3239,\n",
       " 3060,\n",
       " 2936,\n",
       " 4975,\n",
       " 4093,\n",
       " 5735,\n",
       " 4013,\n",
       " 5764,\n",
       " 6378,\n",
       " 8173,\n",
       " 3770,\n",
       " 5020,\n",
       " 7710,\n",
       " 5170,\n",
       " 6180,\n",
       " 2995,\n",
       " 2927,\n",
       " 4062,\n",
       " 1719,\n",
       " 2377,\n",
       " 3465,\n",
       " 3850,\n",
       " 1805,\n",
       " 43429,\n",
       " 2233,\n",
       " 27842,\n",
       " 5323,\n",
       " 2781,\n",
       " 30381,\n",
       " 5111,\n",
       " 4293,\n",
       " 4797,\n",
       " 5016,\n",
       " 6029,\n",
       " 3501,\n",
       " 4855,\n",
       " 5343,\n",
       " 6706,\n",
       " 5560,\n",
       " 6173,\n",
       " 2827,\n",
       " 3471,\n",
       " 2945,\n",
       " 9434,\n",
       " 3500,\n",
       " 608,\n",
       " 3679,\n",
       " 35554,\n",
       " 4883,\n",
       " 3642,\n",
       " 5559,\n",
       " 4545,\n",
       " 6228,\n",
       " 3424,\n",
       " 5100,\n",
       " 2542,\n",
       " 3416,\n",
       " 5646,\n",
       " 4771,\n",
       " 8760,\n",
       " 5146,\n",
       " 3722,\n",
       " 4854,\n",
       " 3690,\n",
       " 3828,\n",
       " 6431,\n",
       " 4235,\n",
       " 4976,\n",
       " 32082,\n",
       " 3792,\n",
       " 9165,\n",
       " 8760,\n",
       " 3803,\n",
       " 40274,\n",
       " 6499,\n",
       " 8906,\n",
       " 1851,\n",
       " 4100,\n",
       " 24888,\n",
       " 3870,\n",
       " 4867,\n",
       " 23818,\n",
       " 4251,\n",
       " 4698,\n",
       " 3368,\n",
       " 4563,\n",
       " 3501,\n",
       " 5972,\n",
       " 4911,\n",
       " 5077,\n",
       " 2867,\n",
       " 4192,\n",
       " 3180,\n",
       " 18521,\n",
       " 4814,\n",
       " 512,\n",
       " 3187,\n",
       " 10270,\n",
       " 5495,\n",
       " 6341,\n",
       " 6143,\n",
       " 3565,\n",
       " 4430,\n",
       " 4320,\n",
       " 2602,\n",
       " 3165,\n",
       " 2667,\n",
       " 5583,\n",
       " 3442,\n",
       " 10311,\n",
       " 4251,\n",
       " 6079,\n",
       " 3964,\n",
       " 3622,\n",
       " 7448,\n",
       " 3030,\n",
       " 4109,\n",
       " 6954,\n",
       " 18609,\n",
       " 5463,\n",
       " 5984,\n",
       " 5744,\n",
       " 2278,\n",
       " 28189,\n",
       " 1478,\n",
       " 1581,\n",
       " 2479,\n",
       " 24057,\n",
       " 22885,\n",
       " 20239,\n",
       " 11479,\n",
       " 4051,\n",
       " 1715,\n",
       " 4733,\n",
       " 3795,\n",
       " 5578,\n",
       " 6653,\n",
       " 5147,\n",
       " 4508,\n",
       " 6056,\n",
       " 2745,\n",
       " 3291,\n",
       " 5435,\n",
       " 1450,\n",
       " 3993,\n",
       " 686,\n",
       " 3895,\n",
       " 9203,\n",
       " 4554,\n",
       " 4909,\n",
       " 5016,\n",
       " 4544,\n",
       " 2729,\n",
       " 4179,\n",
       " 3019,\n",
       " 3200,\n",
       " 3498,\n",
       " 4426,\n",
       " 3967,\n",
       " 4639,\n",
       " 7316,\n",
       " 3707,\n",
       " 7425,\n",
       " 7045,\n",
       " 14905,\n",
       " 2504,\n",
       " 1907,\n",
       " 6041,\n",
       " 1873,\n",
       " 3730,\n",
       " 4118,\n",
       " 4440,\n",
       " 1348,\n",
       " 49268,\n",
       " 2175,\n",
       " 1574,\n",
       " 2500,\n",
       " 25880,\n",
       " 27911,\n",
       " 21650,\n",
       " 15100,\n",
       " 2603,\n",
       " 1548,\n",
       " 5134,\n",
       " 3807,\n",
       " 6164,\n",
       " 6124,\n",
       " 7294,\n",
       " 4969,\n",
       " 7936,\n",
       " 4191,\n",
       " 3834,\n",
       " 5462,\n",
       " 1650,\n",
       " 3788,\n",
       " 595,\n",
       " 6813,\n",
       " 10964,\n",
       " 4452,\n",
       " 4312,\n",
       " 3177,\n",
       " 4957,\n",
       " 3321,\n",
       " 4229,\n",
       " 4809,\n",
       " 6061,\n",
       " 4571,\n",
       " 4486,\n",
       " 5391,\n",
       " 7265,\n",
       " 9769,\n",
       " 5272,\n",
       " 9918,\n",
       " 4289,\n",
       " 26464,\n",
       " 3696,\n",
       " 1717,\n",
       " 6812,\n",
       " 2798,\n",
       " 4482,\n",
       " 6256,\n",
       " 6466,\n",
       " 2081,\n",
       " 56288,\n",
       " 1276,\n",
       " 1828,\n",
       " 4192,\n",
       " 19658,\n",
       " 27075,\n",
       " 12688,\n",
       " 11712,\n",
       " 2261,\n",
       " 2115,\n",
       " 4650,\n",
       " 3904,\n",
       " 5124,\n",
       " 4973,\n",
       " 6183,\n",
       " 2565,\n",
       " 5576,\n",
       " 2323,\n",
       " 5153,\n",
       " 2826,\n",
       " 1484,\n",
       " 3674,\n",
       " 500,\n",
       " 5053,\n",
       " 9011,\n",
       " 4845,\n",
       " 4240,\n",
       " 4360,\n",
       " 4496,\n",
       " 4855,\n",
       " 2937,\n",
       " 2884,\n",
       " 4507,\n",
       " 11644,\n",
       " 4115,\n",
       " 4106,\n",
       " 4971,\n",
       " 5739,\n",
       " 5083,\n",
       " 2833,\n",
       " 3836,\n",
       " 7544,\n",
       " 3556,\n",
       " 2208,\n",
       " 4850,\n",
       " 2276,\n",
       " 2713,\n",
       " 4786,\n",
       " 4489,\n",
       " 2092,\n",
       " 54374,\n",
       " 1057,\n",
       " 1507,\n",
       " 10689,\n",
       " 18062,\n",
       " 23008,\n",
       " 8333,\n",
       " 15300,\n",
       " 2010,\n",
       " 2075,\n",
       " 4205,\n",
       " 3299,\n",
       " 5210,\n",
       " 5760,\n",
       " 7004,\n",
       " 2870,\n",
       " 4566,\n",
       " 2590,\n",
       " 4306,\n",
       " 2734,\n",
       " 1765,\n",
       " 2682,\n",
       " 457,\n",
       " 5080,\n",
       " 6435,\n",
       " 3402,\n",
       " 3809,\n",
       " 4504,\n",
       " 4098,\n",
       " 4420,\n",
       " 2452,\n",
       " 4383,\n",
       " 3322,\n",
       " 20345,\n",
       " 4187,\n",
       " 4172,\n",
       " 4691,\n",
       " 5952,\n",
       " 4419,\n",
       " 2793,\n",
       " 3261,\n",
       " 2756,\n",
       " 4321,\n",
       " 2386,\n",
       " 5274,\n",
       " 2916,\n",
       " 4263,\n",
       " 5807,\n",
       " 6220,\n",
       " 2249,\n",
       " 57645,\n",
       " 1509,\n",
       " 1352,\n",
       " 11641,\n",
       " 15444,\n",
       " 23435,\n",
       " 6641,\n",
       " 20251,\n",
       " 2771,\n",
       " 1981,\n",
       " 5092,\n",
       " 4436,\n",
       " 6162,\n",
       " 3652,\n",
       " 6669,\n",
       " 2450,\n",
       " 6528,\n",
       " 3314,\n",
       " 5747,\n",
       " 2465,\n",
       " 1601,\n",
       " 3870,\n",
       " 570,\n",
       " 5324,\n",
       " 8545,\n",
       " 2793,\n",
       " 5768,\n",
       " 5880,\n",
       " 3900,\n",
       " 4644,\n",
       " 2510,\n",
       " 3371,\n",
       " 4114,\n",
       " 16604,\n",
       " 5216,\n",
       " 5736,\n",
       " 6220,\n",
       " 3720,\n",
       " 3559,\n",
       " 3101,\n",
       " 3315,\n",
       " 2156,\n",
       " 3159,\n",
       " 1588,\n",
       " 4395,\n",
       " 2370,\n",
       " 4763,\n",
       " 3781,\n",
       " 7173,\n",
       " 1952,\n",
       " 53751,\n",
       " 866,\n",
       " 1466,\n",
       " 10580,\n",
       " 17782,\n",
       " 23322,\n",
       " 7822,\n",
       " 10122,\n",
       " 2468,\n",
       " 8961,\n",
       " 4562,\n",
       " 3239,\n",
       " 3424,\n",
       " 3918,\n",
       " 4658,\n",
       " 2946,\n",
       " 5560,\n",
       " 1776,\n",
       " 3482,\n",
       " 2894,\n",
       " 1720,\n",
       " 2842,\n",
       " 390,\n",
       " 6152,\n",
       " 6064,\n",
       " 4076,\n",
       " 4570,\n",
       " 6206,\n",
       " 2963,\n",
       " 3133,\n",
       " 2408,\n",
       " 3929,\n",
       " 3385,\n",
       " 14903,\n",
       " 3921,\n",
       " 4337,\n",
       " 5165,\n",
       " 4163,\n",
       " 3002,\n",
       " 3047,\n",
       " 4708,\n",
       " 1953,\n",
       " 3048,\n",
       " 1585,\n",
       " 5585,\n",
       " 3007,\n",
       " 3564,\n",
       " 2829,\n",
       " 6075,\n",
       " 1634,\n",
       " 46240,\n",
       " 1673,\n",
       " 2135,\n",
       " 7047,\n",
       " 25174,\n",
       " 27188,\n",
       " 11813,\n",
       " 7752,\n",
       " 3040,\n",
       " 6217,\n",
       " 4530,\n",
       " 5020,\n",
       " 5458,\n",
       " 3945,\n",
       " 5627,\n",
       " 3470,\n",
       " 5060,\n",
       " 3330,\n",
       " 4954,\n",
       " 2631,\n",
       " 1500,\n",
       " 3142,\n",
       " 706,\n",
       " 4992,\n",
       " 7818,\n",
       " 4462,\n",
       " 7329,\n",
       " 5960,\n",
       " 3712,\n",
       " 2743,\n",
       " 2605,\n",
       " 4049,\n",
       " 3663,\n",
       " 19330,\n",
       " 5015,\n",
       " 5593,\n",
       " 4123,\n",
       " 3942,\n",
       " 2824,\n",
       " 3592,\n",
       " 3677,\n",
       " 2447,\n",
       " 4497,\n",
       " 2756,\n",
       " 4792,\n",
       " 3068,\n",
       " 4527,\n",
       " 3772,\n",
       " 7841,\n",
       " 1692,\n",
       " 43688,\n",
       " 1847,\n",
       " 7767,\n",
       " 8430,\n",
       " 10222,\n",
       " 27623,\n",
       " 14061,\n",
       " 12228,\n",
       " 7299,\n",
       " 9182,\n",
       " 6207,\n",
       " 5461,\n",
       " 5742,\n",
       " 5773,\n",
       " 6784,\n",
       " 3608,\n",
       " 7037,\n",
       " 3476,\n",
       " 5004,\n",
       " 3803,\n",
       " 2039,\n",
       " 4296,\n",
       " 524,\n",
       " 5488,\n",
       " 9678,\n",
       " 3426,\n",
       " 9621,\n",
       " 5035,\n",
       " 3285,\n",
       " 4060,\n",
       " 4559,\n",
       " 3081,\n",
       " 3655,\n",
       " 2972,\n",
       " 4663,\n",
       " 5729,\n",
       " 5089,\n",
       " 5749,\n",
       " 5278,\n",
       " 5202,\n",
       " 4564,\n",
       " 14046,\n",
       " 5615,\n",
       " 4162,\n",
       " 5417,\n",
       " 3134,\n",
       " 4372,\n",
       " 4780,\n",
       " 3249,\n",
       " 1336,\n",
       " 23247,\n",
       " ...]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "our_list"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e3c0831f-dfd8-4d92-81e2-cad4f14f4ffc",
   "metadata": {},
   "source": [
    "### another way using pandas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "9c1602b8-0529-4c65-b3b3-703b4b0a74d2",
   "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>barcode</th>\n",
       "      <th>total</th>\n",
       "      <th>duplicate</th>\n",
       "      <th>chimeric</th>\n",
       "      <th>unmapped</th>\n",
       "      <th>lowmapq</th>\n",
       "      <th>mitochondrial</th>\n",
       "      <th>nonprimary</th>\n",
       "      <th>passed_filters</th>\n",
       "      <th>is__cell_barcode</th>\n",
       "      <th>excluded_reason</th>\n",
       "      <th>TSS_fragments</th>\n",
       "      <th>DNase_sensitive_region_fragments</th>\n",
       "      <th>enhancer_region_fragments</th>\n",
       "      <th>promoter_region_fragments</th>\n",
       "      <th>on_target_fragments</th>\n",
       "      <th>blacklist_region_fragments</th>\n",
       "      <th>peak_region_fragments</th>\n",
       "      <th>peak_region_cutsites</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AAACATCGAAACATCG-1</td>\n",
       "      <td>485</td>\n",
       "      <td>40</td>\n",
       "      <td>0</td>\n",
       "      <td>76</td>\n",
       "      <td>40</td>\n",
       "      <td>26</td>\n",
       "      <td>0</td>\n",
       "      <td>303</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>104</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>104</td>\n",
       "      <td>0</td>\n",
       "      <td>108</td>\n",
       "      <td>211</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AAACATCGAACAACCA-1</td>\n",
       "      <td>4476</td>\n",
       "      <td>528</td>\n",
       "      <td>2</td>\n",
       "      <td>577</td>\n",
       "      <td>351</td>\n",
       "      <td>203</td>\n",
       "      <td>0</td>\n",
       "      <td>2815</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>886</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>886</td>\n",
       "      <td>0</td>\n",
       "      <td>921</td>\n",
       "      <td>1766</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AAACATCGAACCGAGA-1</td>\n",
       "      <td>6445</td>\n",
       "      <td>849</td>\n",
       "      <td>0</td>\n",
       "      <td>803</td>\n",
       "      <td>482</td>\n",
       "      <td>177</td>\n",
       "      <td>1</td>\n",
       "      <td>4133</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1145</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1145</td>\n",
       "      <td>0</td>\n",
       "      <td>1156</td>\n",
       "      <td>2206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AAACATCGAACGCTTA-1</td>\n",
       "      <td>6341</td>\n",
       "      <td>730</td>\n",
       "      <td>1</td>\n",
       "      <td>879</td>\n",
       "      <td>536</td>\n",
       "      <td>130</td>\n",
       "      <td>0</td>\n",
       "      <td>4065</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1053</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1053</td>\n",
       "      <td>0</td>\n",
       "      <td>1045</td>\n",
       "      <td>1991</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AAACATCGAACGTGAT-1</td>\n",
       "      <td>38717</td>\n",
       "      <td>5060</td>\n",
       "      <td>2</td>\n",
       "      <td>4359</td>\n",
       "      <td>2750</td>\n",
       "      <td>524</td>\n",
       "      <td>3</td>\n",
       "      <td>26019</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>7595</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>7595</td>\n",
       "      <td>0</td>\n",
       "      <td>7847</td>\n",
       "      <td>15000</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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2495</th>\n",
       "      <td>GCCACATAGAATCTGA-1</td>\n",
       "      <td>11735</td>\n",
       "      <td>1299</td>\n",
       "      <td>1</td>\n",
       "      <td>2132</td>\n",
       "      <td>919</td>\n",
       "      <td>379</td>\n",
       "      <td>0</td>\n",
       "      <td>7005</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1858</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1858</td>\n",
       "      <td>0</td>\n",
       "      <td>1979</td>\n",
       "      <td>3786</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2496</th>\n",
       "      <td>GCCACATAGACTAGTA-1</td>\n",
       "      <td>17777</td>\n",
       "      <td>2247</td>\n",
       "      <td>2</td>\n",
       "      <td>2408</td>\n",
       "      <td>1395</td>\n",
       "      <td>477</td>\n",
       "      <td>2</td>\n",
       "      <td>11246</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2874</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2874</td>\n",
       "      <td>0</td>\n",
       "      <td>2822</td>\n",
       "      <td>5362</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2497</th>\n",
       "      <td>GCCACATAGAGCTGAA-1</td>\n",
       "      <td>12042</td>\n",
       "      <td>1164</td>\n",
       "      <td>1</td>\n",
       "      <td>2475</td>\n",
       "      <td>921</td>\n",
       "      <td>480</td>\n",
       "      <td>0</td>\n",
       "      <td>7001</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1803</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1803</td>\n",
       "      <td>0</td>\n",
       "      <td>1868</td>\n",
       "      <td>3573</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2498</th>\n",
       "      <td>GCCACATAGATAGACA-1</td>\n",
       "      <td>6408</td>\n",
       "      <td>708</td>\n",
       "      <td>0</td>\n",
       "      <td>1077</td>\n",
       "      <td>545</td>\n",
       "      <td>226</td>\n",
       "      <td>1</td>\n",
       "      <td>3851</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>929</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>929</td>\n",
       "      <td>0</td>\n",
       "      <td>880</td>\n",
       "      <td>1660</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2499</th>\n",
       "      <td>GCCACATAGCCACATA-1</td>\n",
       "      <td>24720</td>\n",
       "      <td>2448</td>\n",
       "      <td>0</td>\n",
       "      <td>3928</td>\n",
       "      <td>2044</td>\n",
       "      <td>724</td>\n",
       "      <td>4</td>\n",
       "      <td>15572</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>4248</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4248</td>\n",
       "      <td>0</td>\n",
       "      <td>4275</td>\n",
       "      <td>8144</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2500 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 barcode  total  duplicate  chimeric  unmapped  lowmapq  \\\n",
       "0     AAACATCGAAACATCG-1    485         40         0        76       40   \n",
       "1     AAACATCGAACAACCA-1   4476        528         2       577      351   \n",
       "2     AAACATCGAACCGAGA-1   6445        849         0       803      482   \n",
       "3     AAACATCGAACGCTTA-1   6341        730         1       879      536   \n",
       "4     AAACATCGAACGTGAT-1  38717       5060         2      4359     2750   \n",
       "...                  ...    ...        ...       ...       ...      ...   \n",
       "2495  GCCACATAGAATCTGA-1  11735       1299         1      2132      919   \n",
       "2496  GCCACATAGACTAGTA-1  17777       2247         2      2408     1395   \n",
       "2497  GCCACATAGAGCTGAA-1  12042       1164         1      2475      921   \n",
       "2498  GCCACATAGATAGACA-1   6408        708         0      1077      545   \n",
       "2499  GCCACATAGCCACATA-1  24720       2448         0      3928     2044   \n",
       "\n",
       "      mitochondrial  nonprimary  passed_filters  is__cell_barcode  \\\n",
       "0                26           0             303                 0   \n",
       "1               203           0            2815                 0   \n",
       "2               177           1            4133                 0   \n",
       "3               130           0            4065                 0   \n",
       "4               524           3           26019                 1   \n",
       "...             ...         ...             ...               ...   \n",
       "2495            379           0            7005                 0   \n",
       "2496            477           2           11246                 0   \n",
       "2497            480           0            7001                 0   \n",
       "2498            226           1            3851                 0   \n",
       "2499            724           4           15572                 1   \n",
       "\n",
       "      excluded_reason  TSS_fragments  DNase_sensitive_region_fragments  \\\n",
       "0                   3            104                                 0   \n",
       "1                   3            886                                 0   \n",
       "2                   3           1145                                 0   \n",
       "3                   3           1053                                 0   \n",
       "4                   0           7595                                 0   \n",
       "...               ...            ...                               ...   \n",
       "2495                3           1858                                 0   \n",
       "2496                0           2874                                 0   \n",
       "2497                3           1803                                 0   \n",
       "2498                3            929                                 0   \n",
       "2499                0           4248                                 0   \n",
       "\n",
       "      enhancer_region_fragments  promoter_region_fragments  \\\n",
       "0                             0                          0   \n",
       "1                             0                          0   \n",
       "2                             0                          0   \n",
       "3                             0                          0   \n",
       "4                             0                          0   \n",
       "...                         ...                        ...   \n",
       "2495                          0                          0   \n",
       "2496                          0                          0   \n",
       "2497                          0                          0   \n",
       "2498                          0                          0   \n",
       "2499                          0                          0   \n",
       "\n",
       "      on_target_fragments  blacklist_region_fragments  peak_region_fragments  \\\n",
       "0                     104                           0                    108   \n",
       "1                     886                           0                    921   \n",
       "2                    1145                           0                   1156   \n",
       "3                    1053                           0                   1045   \n",
       "4                    7595                           0                   7847   \n",
       "...                   ...                         ...                    ...   \n",
       "2495                 1858                           0                   1979   \n",
       "2496                 2874                           0                   2822   \n",
       "2497                 1803                           0                   1868   \n",
       "2498                  929                           0                    880   \n",
       "2499                 4248                           0                   4275   \n",
       "\n",
       "      peak_region_cutsites  \n",
       "0                      211  \n",
       "1                     1766  \n",
       "2                     2206  \n",
       "3                     1991  \n",
       "4                    15000  \n",
       "...                    ...  \n",
       "2495                  3786  \n",
       "2496                  5362  \n",
       "2497                  3573  \n",
       "2498                  1660  \n",
       "2499                  8144  \n",
       "\n",
       "[2500 rows x 19 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "input_mtx=pd.read_csv('ATAC_meta.csv')\n",
    "input_mtx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "7246c61c-b659-4c6b-82b2-c64b2a39fa55",
   "metadata": {},
   "outputs": [],
   "source": [
    "our_list_pandas=list(input_mtx['total'])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b48d9df1-0bd7-4875-ac48-996c13e35129",
   "metadata": {},
   "source": [
    "## 2. Count how many lines there are in this .csv file and calculate the average of the list you obtained."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "907c2989-22e2-4fd7-9468-b183db9a6028",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2500\n"
     ]
    }
   ],
   "source": [
    "input_file=open('ATAC_meta.csv', 'r')\n",
    "input_file.readline()\n",
    "print(len(input_file.readlines()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "d29c9075-7d28-48c0-8dc0-74da5086957d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2500\n",
      "2500\n"
     ]
    }
   ],
   "source": [
    "print(len(our_list))\n",
    "print(len(our_list_pandas))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "f2d1d969-bc60-45ff-b08d-e38c07e7fc88",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7273.056\n",
      "7273.056\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "print(np.mean(our_list))\n",
    "print(np.mean(our_list_pandas))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1ac44cee-b31e-4ebf-bd32-83e15be92837",
   "metadata": {},
   "source": [
    "## 3. write a Python script that can generate a reverse complement sequence for any sequences containing A/C/T/G"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "39aa0f9d-f751-469c-8dff-59ef6edbd0e0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'GGCCTTAA'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\"AATTCCGG\"[::-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "1691126e-f71e-4ce3-9c3d-396617509d0a",
   "metadata": {},
   "outputs": [],
   "source": [
    "def reverse_complement(seq):\n",
    "    \"\"\"\n",
    "    This function takes a DNA sequence as input and returns its reverse complement.\n",
    "    \"\"\"\n",
    "    complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}\n",
    "    new_seq = []\n",
    "    for base in seq[::-1]:\n",
    "        new_seq.append(complement[base])\n",
    "    return ''.join(new_seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "9aa31037-a1b9-43bc-99c3-7f41f489b875",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CCGGAATT\n"
     ]
    }
   ],
   "source": [
    "seq = \"AATTCCGG\"\n",
    "print(reverse_complement(seq))"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.12.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}