scratchpad_for_calculate_averages_stddev.py.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#This is a scratch pad for writing the first version of the 'calculate_averages_stddev.py' script"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import math"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset = pd.read_excel(\"/home/dolley/gear_datasets/Hertzano_Lab/RiboTag ZF dataset_filtered.xlsx\", index_col=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                              Gene_ID      IN1_CPM      IN2_CPM      IN3_CPM  \\\n",
      "Gene_name                                                                      \n",
      "grin2db            ENSDARG00000070620     0.405251     0.361940     0.389655   \n",
      "cnga3b             ENSDARG00000012297     1.063784     1.085820     1.091034   \n",
      "si:ch211-196j1.2p  ENSDARG00000095475     0.126641     0.114297     0.140276   \n",
      "cnga3a             ENSDARG00000070726     2.760772     2.552629     2.945793   \n",
      "zbtb20             ENSDARG00000005586     0.101313     0.152396     0.015586   \n",
      "CABZ01117436.1     ENSDARG00000103864     0.050656     0.057148     0.093517   \n",
      "abhd2a             ENSDARG00000025797     0.126641     0.152396     0.155862   \n",
      "si:dkey-202p8.1    ENSDARG00000093232     0.177297     0.152396     0.109103   \n",
      "onecut1            ENSDARG00000007982     1.494363     0.704830     0.561103   \n",
      "tmc2a              ENSDARG00000033104     0.177297     0.476237     0.296138   \n",
      "c3a.5              ENSDARG00000053462     0.025328     0.019049     0.031172   \n",
      "kdm6bb             ENSDARG00000056929     5.217605     3.695597     3.522483   \n",
      "si:dkey-217f16.2   ENSDARG00000093487     0.025328     0.057148     0.077931   \n",
      "loxhd1b            ENSDARG00000074638     0.633204     0.704830     0.904000   \n",
      "tsen54             ENSDARG00000036844     0.683861     1.123919     0.966345   \n",
      "malat1             ENSDARG00000099970   505.297186   620.593631  1052.879400   \n",
      "CR735126.1         ENSDARG00000044212     3.571273     3.695597     9.819310   \n",
      "tnks1bp1           ENSDARG00000068760    28.519530    46.194965    61.581101   \n",
      "wu:fi09b08         ENSDARG00000087953   109.240439     1.771601    42.971170   \n",
      "si:dkey-73p2.5     ENSDARG00000096831     0.101313     0.266693     0.249379   \n",
      "ago2               ENSDARG00000061268     0.253282     0.095247     0.077931   \n",
      "rab11fip1b         ENSDARG00000036462     3.039382     3.924191     2.727586   \n",
      "si:dkey-217f16.1   ENSDARG00000089602     0.050656     0.190495     0.062345   \n",
      "loxhd1a            ENSDARG00000094738     0.050656     0.133346     0.202621   \n",
      "si:dkey-242k1.6    ENSDARG00000101205     0.075985     0.133346     0.140276   \n",
      "camta1             ENSDARG00000105435     0.050656     0.057148     0.062345   \n",
      "BX322612.1         ENSDARG00000099968     0.101313     0.114297     0.171448   \n",
      "si:ch211-284k5.2   ENSDARG00000101455     0.354595     0.400039     0.639034   \n",
      "csrnp2             ENSDARG00000075972     0.101313     0.152396     0.077931   \n",
      "cnga1              ENSDARG00000012125     0.506564     0.647682     1.870345   \n",
      "...                               ...          ...          ...          ...   \n",
      "mt-co1             ENSDARG00000063905  2490.747869  2501.366847  2219.444587   \n",
      "mt-atp6            ENSDARG00000063911  1152.229554  1372.019022  1055.622572   \n",
      "plppr1             ENSDARG00000100642     7.953048     8.076975     5.922758   \n",
      "si:ch211-153n19.3  ENSDARG00000105638    28.696828    30.650597    19.685378   \n",
      "matn3a             ENSDARG00000069245    31.837522    22.554572    23.379309   \n",
      "jagn1a             ENSDARG00000041071     4.457760     4.571873     4.364138   \n",
      "sypa               ENSDARG00000042974    24.770960    17.792205    11.362344   \n",
      "CABZ01067681.1     ENSDARG00000103190    10.485866    12.172611     8.307448   \n",
      "si:dkey-183j2.10   ENSDARG00000070511     9.346098     9.562834    10.551862   \n",
      "si:ch211-214j24.9  ENSDARG00000015931    47.414353    43.889979    35.645654   \n",
      "tsg101a            ENSDARG00000040854     7.218531     7.448343     6.078620   \n",
      "capn2l             ENSDARG00000034211     8.510268     8.743707     6.312414   \n",
      "sv2bb              ENSDARG00000060711    12.233511    11.296336     6.592965   \n",
      "zgc:165461         ENSDARG00000040162    14.741001    15.811060    24.376826   \n",
      "serpini1           ENSDARG00000034168     7.395828     7.162601     2.961379   \n",
      "letmd1             ENSDARG00000030641    14.639688    19.601905    16.833103   \n",
      "syngr3a            ENSDARG00000014871    16.032738    15.182428     6.655310   \n",
      "rab10              ENSDARG00000046106    32.217445    39.318106    31.749102   \n",
      "dpagt1             ENSDARG00000061061     4.305791     4.933813     3.912138   \n",
      "ceacam1            ENSDARG00000041119    21.427640    18.039848    15.601792   \n",
      "fh                 ENSDARG00000075132     6.357373     7.410244     9.912827   \n",
      "tnw                ENSDARG00000097594     6.357373     6.800661     4.504414   \n",
      "crx                ENSDARG00000097813    15.602159    16.534940    13.201517   \n",
      "si:ch211-147f12.7  ENSDARG00000097678    12.410808    12.953640    11.736413   \n",
      "tmem168a           ENSDARG00000068705     3.596602     2.819322     2.743172   \n",
      "ric8b              ENSDARG00000005972     7.801079     9.010399     6.374758   \n",
      "pdha1b             ENSDARG00000010555     2.963397     3.828943     3.584827   \n",
      "irf2bp2a           ENSDARG00000004702    19.173432    18.725629    17.643585   \n",
      "si:ch211-202p1.4   ENSDARG00000096675     7.041234     7.695986     6.842345   \n",
      "cmn                ENSDARG00000055527    13.398607     7.753134    10.224551   \n",
      "\n",
      "                        IP1_CPM       IP2_CPM       IP3_CPM  DESeqFC_IP/IN  \\\n",
      "Gene_name                                                                    \n",
      "grin2db               16.289409     25.783672     47.811166     238.450726   \n",
      "cnga3b                41.414296     44.357220    114.784494     171.145028   \n",
      "si:ch211-196j1.2p      5.558319      5.881070      8.355959     140.542532   \n",
      "cnga3a                54.298030     79.909449    184.176653     120.512588   \n",
      "zbtb20                 4.465933      3.322638      4.586354     109.137919   \n",
      "CABZ01117436.1         3.983997      3.322638      3.643952     108.301435   \n",
      "abhd2a                 4.562320      5.415900      6.533983     105.047173   \n",
      "si:dkey-202p8.1        3.245030      2.990374      5.874302      98.878740   \n",
      "onecut1               29.398046     26.813690     19.130749      87.784253   \n",
      "tmc2a                  6.714963      7.974332     10.020869      85.964033   \n",
      "c3a.5                  0.610451      0.498396      0.691094      84.531997   \n",
      "kdm6bb                59.663575     86.122782    142.239789      83.536804   \n",
      "si:dkey-217f16.2       0.385548      1.495187      2.198937      79.719269   \n",
      "loxhd1b               11.984121     13.257326     26.041693      77.354843   \n",
      "tsen54                17.446053     14.220892     37.633230      76.456421   \n",
      "malat1             17244.443753  14029.407873  32123.291992      74.470092   \n",
      "CR735126.1           124.756952     98.881713    231.014004      67.599114   \n",
      "tnks1bp1             582.145561    774.938908   1863.316107      65.117677   \n",
      "wu:fi09b08           656.202933   1695.243238   1996.257535      55.900177   \n",
      "si:dkey-73p2.5         2.024128      1.594866      5.842889      55.218546   \n",
      "ago2                   2.249031      2.890695      1.759149      53.500537   \n",
      "rab11fip1b            42.860101     44.423673     54.910590      50.795805   \n",
      "si:dkey-217f16.1       1.060257      1.096471      2.450244      50.019160   \n",
      "loxhd1a                1.702838      1.794225      2.795791      47.780062   \n",
      "si:dkey-242k1.6        2.120515      2.259394      3.392645      46.817407   \n",
      "camta1                 0.610451      0.066453      0.973815      45.973516   \n",
      "BX322612.1             2.377547      2.525205      2.356004      45.599014   \n",
      "si:ch211-284k5.2      13.108637      8.572407      5.937129      45.304755   \n",
      "csrnp2                 0.963870      0.465169      2.136110      44.363620   \n",
      "cnga1                 16.000248     16.646417     22.366327      43.513005   \n",
      "...                         ...           ...           ...            ...   \n",
      "mt-co1                71.551309     30.601498     35.151573       0.060494   \n",
      "mt-atp6               37.590944     21.397790     11.026097       0.060023   \n",
      "plppr1                 0.353419      0.132906      0.031413       0.059231   \n",
      "si:ch211-153n19.3      0.417677      0.431943      0.408374       0.058169   \n",
      "matn3a                 1.188773      0.431943      0.219894       0.056611   \n",
      "jagn1a                 0.128516      0.099679      0.031413       0.056165   \n",
      "sypa                   0.514064      0.332264      0.094240       0.055349   \n",
      "CABZ01067681.1         0.321290      0.066453      0.157067       0.055233   \n",
      "si:dkey-183j2.10       0.257032      0.099679      0.157067       0.054717   \n",
      "si:ch211-214j24.9      0.642580      0.199358      0.942401       0.054194   \n",
      "tsg101a                0.032129      0.132906      0.094240       0.053371   \n",
      "capn2l                 0.160645      0.099679      0.125654       0.052891   \n",
      "sv2bb                  0.064258      0.033226      0.219894       0.050890   \n",
      "zgc:165461             0.417677      0.498396      0.125654       0.050333   \n",
      "serpini1               0.192774      0.066453      0.031413       0.049752   \n",
      "letmd1                 0.096387      0.099679      0.439787       0.049589   \n",
      "syngr3a                0.514064      0.099679      0.062827       0.049477   \n",
      "rab10                  0.706838      0.631301      0.251307       0.047085   \n",
      "dpagt1                 0.128516      0.066453      0.031413       0.046683   \n",
      "ceacam1                0.481935      0.332264      0.094240       0.045564   \n",
      "fh                     0.321290      0.033226      0.094240       0.045239   \n",
      "tnw                    0.128516      0.099679      0.031413       0.043231   \n",
      "crx                    0.224903      0.199358      0.125654       0.042083   \n",
      "si:ch211-147f12.7      0.224903      0.132906      0.125654       0.039194   \n",
      "tmem168a               0.032129      0.033226      0.031413       0.038727   \n",
      "ric8b                  0.192774      0.099679      0.031413       0.036938   \n",
      "pdha1b                 0.064258      0.033226      0.031413       0.034951   \n",
      "irf2bp2a               0.481935      0.099679      0.125654       0.033406   \n",
      "si:ch211-202p1.4       0.224903      0.033226      0.031413       0.031549   \n",
      "cmn                    0.096387      0.033226      0.031413       0.012325   \n",
      "\n",
      "                   DESeqLFC_IP/IN       p-value           FDR  \n",
      "Gene_name                                                      \n",
      "grin2db                  7.897547  2.578124e-79  6.859872e-75  \n",
      "cnga3b                   7.419076  4.316954e-58  2.871638e-54  \n",
      "si:ch211-196j1.2p        7.134863  3.260787e-59  2.892101e-55  \n",
      "cnga3a                   6.913040  9.338086e-42  1.380377e-38  \n",
      "zbtb20                   6.770009  2.091651e-44  3.975331e-41  \n",
      "CABZ01117436.1           6.758909  3.393502e-40  4.514716e-37  \n",
      "abhd2a                   6.714894  8.754250e-51  2.588145e-47  \n",
      "si:dkey-202p8.1          6.627588  1.966205e-42  3.077458e-39  \n",
      "onecut1                  6.455890  8.770674e-71  1.166850e-66  \n",
      "tmc2a                    6.425661  5.801104e-55  2.205082e-51  \n",
      "c3a.5                    6.401426  1.069426e-08  3.046604e-07  \n",
      "kdm6bb                   6.384340  4.884779e-40  6.189247e-37  \n",
      "si:dkey-217f16.2         6.316857  2.975559e-16  3.412659e-14  \n",
      "loxhd1b                  6.273420  3.014898e-57  1.604408e-53  \n",
      "tsen54                   6.256566  7.427525e-56  3.293860e-52  \n",
      "malat1                   6.218589  7.544888e-01  9.661029e-01  \n",
      "CR735126.1               6.078932  5.211682e-29  2.889009e-26  \n",
      "tnks1bp1                 6.024977  3.077233e-06  4.716533e-05  \n",
      "wu:fi09b08               5.804781  6.297512e-05  6.497255e-04  \n",
      "si:dkey-73p2.5           5.787081  1.696647e-28  8.360069e-26  \n",
      "ago2                     5.741481  1.029575e-23  3.010431e-21  \n",
      "rab11fip1b               5.666637  3.750576e-44  6.653022e-41  \n",
      "si:dkey-217f16.1         5.644409  1.349458e-15  1.365261e-13  \n",
      "loxhd1a                  5.578337  8.838342e-20  1.633129e-17  \n",
      "si:dkey-242k1.6          5.548973  1.743279e-23  5.041866e-21  \n",
      "camta1                   5.522731  6.045227e-07  1.111620e-05  \n",
      "BX322612.1               5.510931  2.712253e-22  6.808266e-20  \n",
      "si:ch211-284k5.2         5.501591  1.164983e-49  3.099788e-46  \n",
      "csrnp2                   5.471305  3.048619e-12  1.778896e-10  \n",
      "cnga1                    5.443375  1.881036e-45  4.170883e-42  \n",
      "...                           ...           ...           ...  \n",
      "mt-co1                  -4.047060  2.356882e-05  2.760207e-04  \n",
      "mt-atp6                 -4.058336  5.533184e-09  1.696163e-07  \n",
      "plppr1                  -4.077493  5.562936e-13  3.709739e-11  \n",
      "si:ch211-153n19.3       -4.103595  4.667615e-29  2.642466e-26  \n",
      "matn3a                  -4.142770  4.589272e-27  2.000758e-24  \n",
      "jagn1a                  -4.154197  2.101125e-09  7.007850e-08  \n",
      "sypa                    -4.175287  1.197034e-22  3.185068e-20  \n",
      "CABZ01067681.1          -4.178323  7.186142e-18  1.033561e-15  \n",
      "si:dkey-183j2.10        -4.191872  1.962659e-18  3.090085e-16  \n",
      "si:ch211-214j24.9       -4.205720  4.304810e-34  3.949737e-31  \n",
      "tsg101a                 -4.227804  7.210324e-14  5.692946e-12  \n",
      "capn2l                  -4.240842  2.439700e-16  2.810196e-14  \n",
      "sv2bb                   -4.296485  9.125315e-19  1.471554e-16  \n",
      "zgc:165461              -4.312349  7.793384e-28  3.749249e-25  \n",
      "serpini1                -4.329092  2.063496e-10  8.687578e-09  \n",
      "letmd1                  -4.333835  1.027818e-29  6.670289e-27  \n",
      "syngr3a                 -4.337086  2.004721e-18  3.137743e-16  \n",
      "rab10                   -4.408589  1.780811e-32  1.353823e-29  \n",
      "dpagt1                  -4.420954  5.418708e-10  2.074547e-08  \n",
      "ceacam1                 -4.455977  1.367349e-26  5.350355e-24  \n",
      "fh                      -4.466277  4.102248e-17  5.273073e-15  \n",
      "tnw                     -4.531779  1.105582e-12  7.004124e-11  \n",
      "crx                     -4.570615  6.873806e-25  2.203593e-22  \n",
      "si:ch211-147f12.7       -4.673237  2.477489e-24  7.665236e-22  \n",
      "tmem168a                -4.690514  1.603946e-07  3.438983e-06  \n",
      "ric8b                   -4.758765  1.030810e-16  1.252410e-14  \n",
      "pdha1b                  -4.838514  1.830123e-09  6.227100e-08  \n",
      "irf2bp2a                -4.903756  3.107645e-29  1.879278e-26  \n",
      "si:ch211-202p1.4        -4.986256  3.915236e-16  4.358854e-14  \n",
      "cmn                     -6.342309  2.456732e-29  1.520203e-26  \n",
      "\n",
      "[17211 rows x 11 columns]\n"
     ]
    }
   ],
   "source": [
    "print(dataset)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Extract replicates into new dataframe."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "metadata": {},
   "outputs": [],
   "source": [
    "columns2avg = ['IN1_CPM', 'IN2_CPM', 'IN3_CPM']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_in_different = dataset.loc[:, columns2avg]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                       IN1_CPM      IN2_CPM      IN3_CPM\n",
      "Gene_name                                               \n",
      "grin2db               0.405251     0.361940     0.389655\n",
      "cnga3b                1.063784     1.085820     1.091034\n",
      "si:ch211-196j1.2p     0.126641     0.114297     0.140276\n",
      "cnga3a                2.760772     2.552629     2.945793\n",
      "zbtb20                0.101313     0.152396     0.015586\n",
      "CABZ01117436.1        0.050656     0.057148     0.093517\n",
      "abhd2a                0.126641     0.152396     0.155862\n",
      "si:dkey-202p8.1       0.177297     0.152396     0.109103\n",
      "onecut1               1.494363     0.704830     0.561103\n",
      "tmc2a                 0.177297     0.476237     0.296138\n",
      "c3a.5                 0.025328     0.019049     0.031172\n",
      "kdm6bb                5.217605     3.695597     3.522483\n",
      "si:dkey-217f16.2      0.025328     0.057148     0.077931\n",
      "loxhd1b               0.633204     0.704830     0.904000\n",
      "tsen54                0.683861     1.123919     0.966345\n",
      "malat1              505.297186   620.593631  1052.879400\n",
      "CR735126.1            3.571273     3.695597     9.819310\n",
      "tnks1bp1             28.519530    46.194965    61.581101\n",
      "wu:fi09b08          109.240439     1.771601    42.971170\n",
      "si:dkey-73p2.5        0.101313     0.266693     0.249379\n",
      "ago2                  0.253282     0.095247     0.077931\n",
      "rab11fip1b            3.039382     3.924191     2.727586\n",
      "si:dkey-217f16.1      0.050656     0.190495     0.062345\n",
      "loxhd1a               0.050656     0.133346     0.202621\n",
      "si:dkey-242k1.6       0.075985     0.133346     0.140276\n",
      "camta1                0.050656     0.057148     0.062345\n",
      "BX322612.1            0.101313     0.114297     0.171448\n",
      "si:ch211-284k5.2      0.354595     0.400039     0.639034\n",
      "csrnp2                0.101313     0.152396     0.077931\n",
      "cnga1                 0.506564     0.647682     1.870345\n",
      "...                        ...          ...          ...\n",
      "mt-co1             2490.747869  2501.366847  2219.444587\n",
      "mt-atp6            1152.229554  1372.019022  1055.622572\n",
      "plppr1                7.953048     8.076975     5.922758\n",
      "si:ch211-153n19.3    28.696828    30.650597    19.685378\n",
      "matn3a               31.837522    22.554572    23.379309\n",
      "jagn1a                4.457760     4.571873     4.364138\n",
      "sypa                 24.770960    17.792205    11.362344\n",
      "CABZ01067681.1       10.485866    12.172611     8.307448\n",
      "si:dkey-183j2.10      9.346098     9.562834    10.551862\n",
      "si:ch211-214j24.9    47.414353    43.889979    35.645654\n",
      "tsg101a               7.218531     7.448343     6.078620\n",
      "capn2l                8.510268     8.743707     6.312414\n",
      "sv2bb                12.233511    11.296336     6.592965\n",
      "zgc:165461           14.741001    15.811060    24.376826\n",
      "serpini1              7.395828     7.162601     2.961379\n",
      "letmd1               14.639688    19.601905    16.833103\n",
      "syngr3a              16.032738    15.182428     6.655310\n",
      "rab10                32.217445    39.318106    31.749102\n",
      "dpagt1                4.305791     4.933813     3.912138\n",
      "ceacam1              21.427640    18.039848    15.601792\n",
      "fh                    6.357373     7.410244     9.912827\n",
      "tnw                   6.357373     6.800661     4.504414\n",
      "crx                  15.602159    16.534940    13.201517\n",
      "si:ch211-147f12.7    12.410808    12.953640    11.736413\n",
      "tmem168a              3.596602     2.819322     2.743172\n",
      "ric8b                 7.801079     9.010399     6.374758\n",
      "pdha1b                2.963397     3.828943     3.584827\n",
      "irf2bp2a             19.173432    18.725629    17.643585\n",
      "si:ch211-202p1.4      7.041234     7.695986     6.842345\n",
      "cmn                  13.398607     7.753134    10.224551\n",
      "\n",
      "[17211 rows x 3 columns]\n"
     ]
    }
   ],
   "source": [
    "print(df_in_different)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_in = dataset.iloc[:,1:4].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                       IN1_CPM      IN2_CPM      IN3_CPM\n",
      "Gene_name                                               \n",
      "grin2db               0.405251     0.361940     0.389655\n",
      "cnga3b                1.063784     1.085820     1.091034\n",
      "si:ch211-196j1.2p     0.126641     0.114297     0.140276\n",
      "cnga3a                2.760772     2.552629     2.945793\n",
      "zbtb20                0.101313     0.152396     0.015586\n",
      "CABZ01117436.1        0.050656     0.057148     0.093517\n",
      "abhd2a                0.126641     0.152396     0.155862\n",
      "si:dkey-202p8.1       0.177297     0.152396     0.109103\n",
      "onecut1               1.494363     0.704830     0.561103\n",
      "tmc2a                 0.177297     0.476237     0.296138\n",
      "c3a.5                 0.025328     0.019049     0.031172\n",
      "kdm6bb                5.217605     3.695597     3.522483\n",
      "si:dkey-217f16.2      0.025328     0.057148     0.077931\n",
      "loxhd1b               0.633204     0.704830     0.904000\n",
      "tsen54                0.683861     1.123919     0.966345\n",
      "malat1              505.297186   620.593631  1052.879400\n",
      "CR735126.1            3.571273     3.695597     9.819310\n",
      "tnks1bp1             28.519530    46.194965    61.581101\n",
      "wu:fi09b08          109.240439     1.771601    42.971170\n",
      "si:dkey-73p2.5        0.101313     0.266693     0.249379\n",
      "ago2                  0.253282     0.095247     0.077931\n",
      "rab11fip1b            3.039382     3.924191     2.727586\n",
      "si:dkey-217f16.1      0.050656     0.190495     0.062345\n",
      "loxhd1a               0.050656     0.133346     0.202621\n",
      "si:dkey-242k1.6       0.075985     0.133346     0.140276\n",
      "camta1                0.050656     0.057148     0.062345\n",
      "BX322612.1            0.101313     0.114297     0.171448\n",
      "si:ch211-284k5.2      0.354595     0.400039     0.639034\n",
      "csrnp2                0.101313     0.152396     0.077931\n",
      "cnga1                 0.506564     0.647682     1.870345\n",
      "...                        ...          ...          ...\n",
      "mt-co1             2490.747869  2501.366847  2219.444587\n",
      "mt-atp6            1152.229554  1372.019022  1055.622572\n",
      "plppr1                7.953048     8.076975     5.922758\n",
      "si:ch211-153n19.3    28.696828    30.650597    19.685378\n",
      "matn3a               31.837522    22.554572    23.379309\n",
      "jagn1a                4.457760     4.571873     4.364138\n",
      "sypa                 24.770960    17.792205    11.362344\n",
      "CABZ01067681.1       10.485866    12.172611     8.307448\n",
      "si:dkey-183j2.10      9.346098     9.562834    10.551862\n",
      "si:ch211-214j24.9    47.414353    43.889979    35.645654\n",
      "tsg101a               7.218531     7.448343     6.078620\n",
      "capn2l                8.510268     8.743707     6.312414\n",
      "sv2bb                12.233511    11.296336     6.592965\n",
      "zgc:165461           14.741001    15.811060    24.376826\n",
      "serpini1              7.395828     7.162601     2.961379\n",
      "letmd1               14.639688    19.601905    16.833103\n",
      "syngr3a              16.032738    15.182428     6.655310\n",
      "rab10                32.217445    39.318106    31.749102\n",
      "dpagt1                4.305791     4.933813     3.912138\n",
      "ceacam1              21.427640    18.039848    15.601792\n",
      "fh                    6.357373     7.410244     9.912827\n",
      "tnw                   6.357373     6.800661     4.504414\n",
      "crx                  15.602159    16.534940    13.201517\n",
      "si:ch211-147f12.7    12.410808    12.953640    11.736413\n",
      "tmem168a              3.596602     2.819322     2.743172\n",
      "ric8b                 7.801079     9.010399     6.374758\n",
      "pdha1b                2.963397     3.828943     3.584827\n",
      "irf2bp2a             19.173432    18.725629    17.643585\n",
      "si:ch211-202p1.4      7.041234     7.695986     6.842345\n",
      "cmn                  13.398607     7.753134    10.224551\n",
      "\n",
      "[17211 rows x 3 columns]\n"
     ]
    }
   ],
   "source": [
    "print(df_in)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Get the average of the replicates and convert it to a DataFrame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_in_avg = df_in.mean(axis=1).rename('IN_Avg').to_frame()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Add Averages to main dataFrame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [],
   "source": [
    "result = pd.concat([dataset, df_in_avg], axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                              Gene_ID      IN1_CPM      IN2_CPM      IN3_CPM  \\\n",
      "Gene_name                                                                      \n",
      "grin2db            ENSDARG00000070620     0.405251     0.361940     0.389655   \n",
      "cnga3b             ENSDARG00000012297     1.063784     1.085820     1.091034   \n",
      "si:ch211-196j1.2p  ENSDARG00000095475     0.126641     0.114297     0.140276   \n",
      "cnga3a             ENSDARG00000070726     2.760772     2.552629     2.945793   \n",
      "zbtb20             ENSDARG00000005586     0.101313     0.152396     0.015586   \n",
      "CABZ01117436.1     ENSDARG00000103864     0.050656     0.057148     0.093517   \n",
      "abhd2a             ENSDARG00000025797     0.126641     0.152396     0.155862   \n",
      "si:dkey-202p8.1    ENSDARG00000093232     0.177297     0.152396     0.109103   \n",
      "onecut1            ENSDARG00000007982     1.494363     0.704830     0.561103   \n",
      "tmc2a              ENSDARG00000033104     0.177297     0.476237     0.296138   \n",
      "c3a.5              ENSDARG00000053462     0.025328     0.019049     0.031172   \n",
      "kdm6bb             ENSDARG00000056929     5.217605     3.695597     3.522483   \n",
      "si:dkey-217f16.2   ENSDARG00000093487     0.025328     0.057148     0.077931   \n",
      "loxhd1b            ENSDARG00000074638     0.633204     0.704830     0.904000   \n",
      "tsen54             ENSDARG00000036844     0.683861     1.123919     0.966345   \n",
      "malat1             ENSDARG00000099970   505.297186   620.593631  1052.879400   \n",
      "CR735126.1         ENSDARG00000044212     3.571273     3.695597     9.819310   \n",
      "tnks1bp1           ENSDARG00000068760    28.519530    46.194965    61.581101   \n",
      "wu:fi09b08         ENSDARG00000087953   109.240439     1.771601    42.971170   \n",
      "si:dkey-73p2.5     ENSDARG00000096831     0.101313     0.266693     0.249379   \n",
      "ago2               ENSDARG00000061268     0.253282     0.095247     0.077931   \n",
      "rab11fip1b         ENSDARG00000036462     3.039382     3.924191     2.727586   \n",
      "si:dkey-217f16.1   ENSDARG00000089602     0.050656     0.190495     0.062345   \n",
      "loxhd1a            ENSDARG00000094738     0.050656     0.133346     0.202621   \n",
      "si:dkey-242k1.6    ENSDARG00000101205     0.075985     0.133346     0.140276   \n",
      "camta1             ENSDARG00000105435     0.050656     0.057148     0.062345   \n",
      "BX322612.1         ENSDARG00000099968     0.101313     0.114297     0.171448   \n",
      "si:ch211-284k5.2   ENSDARG00000101455     0.354595     0.400039     0.639034   \n",
      "csrnp2             ENSDARG00000075972     0.101313     0.152396     0.077931   \n",
      "cnga1              ENSDARG00000012125     0.506564     0.647682     1.870345   \n",
      "...                               ...          ...          ...          ...   \n",
      "mt-co1             ENSDARG00000063905  2490.747869  2501.366847  2219.444587   \n",
      "mt-atp6            ENSDARG00000063911  1152.229554  1372.019022  1055.622572   \n",
      "plppr1             ENSDARG00000100642     7.953048     8.076975     5.922758   \n",
      "si:ch211-153n19.3  ENSDARG00000105638    28.696828    30.650597    19.685378   \n",
      "matn3a             ENSDARG00000069245    31.837522    22.554572    23.379309   \n",
      "jagn1a             ENSDARG00000041071     4.457760     4.571873     4.364138   \n",
      "sypa               ENSDARG00000042974    24.770960    17.792205    11.362344   \n",
      "CABZ01067681.1     ENSDARG00000103190    10.485866    12.172611     8.307448   \n",
      "si:dkey-183j2.10   ENSDARG00000070511     9.346098     9.562834    10.551862   \n",
      "si:ch211-214j24.9  ENSDARG00000015931    47.414353    43.889979    35.645654   \n",
      "tsg101a            ENSDARG00000040854     7.218531     7.448343     6.078620   \n",
      "capn2l             ENSDARG00000034211     8.510268     8.743707     6.312414   \n",
      "sv2bb              ENSDARG00000060711    12.233511    11.296336     6.592965   \n",
      "zgc:165461         ENSDARG00000040162    14.741001    15.811060    24.376826   \n",
      "serpini1           ENSDARG00000034168     7.395828     7.162601     2.961379   \n",
      "letmd1             ENSDARG00000030641    14.639688    19.601905    16.833103   \n",
      "syngr3a            ENSDARG00000014871    16.032738    15.182428     6.655310   \n",
      "rab10              ENSDARG00000046106    32.217445    39.318106    31.749102   \n",
      "dpagt1             ENSDARG00000061061     4.305791     4.933813     3.912138   \n",
      "ceacam1            ENSDARG00000041119    21.427640    18.039848    15.601792   \n",
      "fh                 ENSDARG00000075132     6.357373     7.410244     9.912827   \n",
      "tnw                ENSDARG00000097594     6.357373     6.800661     4.504414   \n",
      "crx                ENSDARG00000097813    15.602159    16.534940    13.201517   \n",
      "si:ch211-147f12.7  ENSDARG00000097678    12.410808    12.953640    11.736413   \n",
      "tmem168a           ENSDARG00000068705     3.596602     2.819322     2.743172   \n",
      "ric8b              ENSDARG00000005972     7.801079     9.010399     6.374758   \n",
      "pdha1b             ENSDARG00000010555     2.963397     3.828943     3.584827   \n",
      "irf2bp2a           ENSDARG00000004702    19.173432    18.725629    17.643585   \n",
      "si:ch211-202p1.4   ENSDARG00000096675     7.041234     7.695986     6.842345   \n",
      "cmn                ENSDARG00000055527    13.398607     7.753134    10.224551   \n",
      "\n",
      "                        IP1_CPM       IP2_CPM       IP3_CPM  DESeqFC_IP/IN  \\\n",
      "Gene_name                                                                    \n",
      "grin2db               16.289409     25.783672     47.811166     238.450726   \n",
      "cnga3b                41.414296     44.357220    114.784494     171.145028   \n",
      "si:ch211-196j1.2p      5.558319      5.881070      8.355959     140.542532   \n",
      "cnga3a                54.298030     79.909449    184.176653     120.512588   \n",
      "zbtb20                 4.465933      3.322638      4.586354     109.137919   \n",
      "CABZ01117436.1         3.983997      3.322638      3.643952     108.301435   \n",
      "abhd2a                 4.562320      5.415900      6.533983     105.047173   \n",
      "si:dkey-202p8.1        3.245030      2.990374      5.874302      98.878740   \n",
      "onecut1               29.398046     26.813690     19.130749      87.784253   \n",
      "tmc2a                  6.714963      7.974332     10.020869      85.964033   \n",
      "c3a.5                  0.610451      0.498396      0.691094      84.531997   \n",
      "kdm6bb                59.663575     86.122782    142.239789      83.536804   \n",
      "si:dkey-217f16.2       0.385548      1.495187      2.198937      79.719269   \n",
      "loxhd1b               11.984121     13.257326     26.041693      77.354843   \n",
      "tsen54                17.446053     14.220892     37.633230      76.456421   \n",
      "malat1             17244.443753  14029.407873  32123.291992      74.470092   \n",
      "CR735126.1           124.756952     98.881713    231.014004      67.599114   \n",
      "tnks1bp1             582.145561    774.938908   1863.316107      65.117677   \n",
      "wu:fi09b08           656.202933   1695.243238   1996.257535      55.900177   \n",
      "si:dkey-73p2.5         2.024128      1.594866      5.842889      55.218546   \n",
      "ago2                   2.249031      2.890695      1.759149      53.500537   \n",
      "rab11fip1b            42.860101     44.423673     54.910590      50.795805   \n",
      "si:dkey-217f16.1       1.060257      1.096471      2.450244      50.019160   \n",
      "loxhd1a                1.702838      1.794225      2.795791      47.780062   \n",
      "si:dkey-242k1.6        2.120515      2.259394      3.392645      46.817407   \n",
      "camta1                 0.610451      0.066453      0.973815      45.973516   \n",
      "BX322612.1             2.377547      2.525205      2.356004      45.599014   \n",
      "si:ch211-284k5.2      13.108637      8.572407      5.937129      45.304755   \n",
      "csrnp2                 0.963870      0.465169      2.136110      44.363620   \n",
      "cnga1                 16.000248     16.646417     22.366327      43.513005   \n",
      "...                         ...           ...           ...            ...   \n",
      "mt-co1                71.551309     30.601498     35.151573       0.060494   \n",
      "mt-atp6               37.590944     21.397790     11.026097       0.060023   \n",
      "plppr1                 0.353419      0.132906      0.031413       0.059231   \n",
      "si:ch211-153n19.3      0.417677      0.431943      0.408374       0.058169   \n",
      "matn3a                 1.188773      0.431943      0.219894       0.056611   \n",
      "jagn1a                 0.128516      0.099679      0.031413       0.056165   \n",
      "sypa                   0.514064      0.332264      0.094240       0.055349   \n",
      "CABZ01067681.1         0.321290      0.066453      0.157067       0.055233   \n",
      "si:dkey-183j2.10       0.257032      0.099679      0.157067       0.054717   \n",
      "si:ch211-214j24.9      0.642580      0.199358      0.942401       0.054194   \n",
      "tsg101a                0.032129      0.132906      0.094240       0.053371   \n",
      "capn2l                 0.160645      0.099679      0.125654       0.052891   \n",
      "sv2bb                  0.064258      0.033226      0.219894       0.050890   \n",
      "zgc:165461             0.417677      0.498396      0.125654       0.050333   \n",
      "serpini1               0.192774      0.066453      0.031413       0.049752   \n",
      "letmd1                 0.096387      0.099679      0.439787       0.049589   \n",
      "syngr3a                0.514064      0.099679      0.062827       0.049477   \n",
      "rab10                  0.706838      0.631301      0.251307       0.047085   \n",
      "dpagt1                 0.128516      0.066453      0.031413       0.046683   \n",
      "ceacam1                0.481935      0.332264      0.094240       0.045564   \n",
      "fh                     0.321290      0.033226      0.094240       0.045239   \n",
      "tnw                    0.128516      0.099679      0.031413       0.043231   \n",
      "crx                    0.224903      0.199358      0.125654       0.042083   \n",
      "si:ch211-147f12.7      0.224903      0.132906      0.125654       0.039194   \n",
      "tmem168a               0.032129      0.033226      0.031413       0.038727   \n",
      "ric8b                  0.192774      0.099679      0.031413       0.036938   \n",
      "pdha1b                 0.064258      0.033226      0.031413       0.034951   \n",
      "irf2bp2a               0.481935      0.099679      0.125654       0.033406   \n",
      "si:ch211-202p1.4       0.224903      0.033226      0.031413       0.031549   \n",
      "cmn                    0.096387      0.033226      0.031413       0.012325   \n",
      "\n",
      "                   DESeqLFC_IP/IN       p-value           FDR       IN_Avg  \n",
      "Gene_name                                                                   \n",
      "grin2db                  7.897547  2.578124e-79  6.859872e-75     0.385615  \n",
      "cnga3b                   7.419076  4.316954e-58  2.871638e-54     1.080213  \n",
      "si:ch211-196j1.2p        7.134863  3.260787e-59  2.892101e-55     0.127071  \n",
      "cnga3a                   6.913040  9.338086e-42  1.380377e-38     2.753065  \n",
      "zbtb20                   6.770009  2.091651e-44  3.975331e-41     0.089765  \n",
      "CABZ01117436.1           6.758909  3.393502e-40  4.514716e-37     0.067107  \n",
      "abhd2a                   6.714894  8.754250e-51  2.588145e-47     0.144966  \n",
      "si:dkey-202p8.1          6.627588  1.966205e-42  3.077458e-39     0.146265  \n",
      "onecut1                  6.455890  8.770674e-71  1.166850e-66     0.920099  \n",
      "tmc2a                    6.425661  5.801104e-55  2.205082e-51     0.316557  \n",
      "c3a.5                    6.401426  1.069426e-08  3.046604e-07     0.025183  \n",
      "kdm6bb                   6.384340  4.884779e-40  6.189247e-37     4.145228  \n",
      "si:dkey-217f16.2         6.316857  2.975559e-16  3.412659e-14     0.053469  \n",
      "loxhd1b                  6.273420  3.014898e-57  1.604408e-53     0.747345  \n",
      "tsen54                   6.256566  7.427525e-56  3.293860e-52     0.924708  \n",
      "malat1                   6.218589  7.544888e-01  9.661029e-01   726.256739  \n",
      "CR735126.1               6.078932  5.211682e-29  2.889009e-26     5.695393  \n",
      "tnks1bp1                 6.024977  3.077233e-06  4.716533e-05    45.431865  \n",
      "wu:fi09b08               5.804781  6.297512e-05  6.497255e-04    51.327737  \n",
      "si:dkey-73p2.5           5.787081  1.696647e-28  8.360069e-26     0.205795  \n",
      "ago2                     5.741481  1.029575e-23  3.010431e-21     0.142153  \n",
      "rab11fip1b               5.666637  3.750576e-44  6.653022e-41     3.230386  \n",
      "si:dkey-217f16.1         5.644409  1.349458e-15  1.365261e-13     0.101165  \n",
      "loxhd1a                  5.578337  8.838342e-20  1.633129e-17     0.128874  \n",
      "si:dkey-242k1.6          5.548973  1.743279e-23  5.041866e-21     0.116536  \n",
      "camta1                   5.522731  6.045227e-07  1.111620e-05     0.056717  \n",
      "BX322612.1               5.510931  2.712253e-22  6.808266e-20     0.129019  \n",
      "si:ch211-284k5.2         5.501591  1.164983e-49  3.099788e-46     0.464556  \n",
      "csrnp2                   5.471305  3.048619e-12  1.778896e-10     0.110547  \n",
      "cnga1                    5.443375  1.881036e-45  4.170883e-42     1.008197  \n",
      "...                           ...           ...           ...          ...  \n",
      "mt-co1                  -4.047060  2.356882e-05  2.760207e-04  2403.853101  \n",
      "mt-atp6                 -4.058336  5.533184e-09  1.696163e-07  1193.290383  \n",
      "plppr1                  -4.077493  5.562936e-13  3.709739e-11     7.317594  \n",
      "si:ch211-153n19.3       -4.103595  4.667615e-29  2.642466e-26    26.344268  \n",
      "matn3a                  -4.142770  4.589272e-27  2.000758e-24    25.923801  \n",
      "jagn1a                  -4.154197  2.101125e-09  7.007850e-08     4.464590  \n",
      "sypa                    -4.175287  1.197034e-22  3.185068e-20    17.975170  \n",
      "CABZ01067681.1          -4.178323  7.186142e-18  1.033561e-15    10.321975  \n",
      "si:dkey-183j2.10        -4.191872  1.962659e-18  3.090085e-16     9.820265  \n",
      "si:ch211-214j24.9       -4.205720  4.304810e-34  3.949737e-31    42.316662  \n",
      "tsg101a                 -4.227804  7.210324e-14  5.692946e-12     6.915165  \n",
      "capn2l                  -4.240842  2.439700e-16  2.810196e-14     7.855463  \n",
      "sv2bb                   -4.296485  9.125315e-19  1.471554e-16    10.040937  \n",
      "zgc:165461              -4.312349  7.793384e-28  3.749249e-25    18.309629  \n",
      "serpini1                -4.329092  2.063496e-10  8.687578e-09     5.839936  \n",
      "letmd1                  -4.333835  1.027818e-29  6.670289e-27    17.024898  \n",
      "syngr3a                 -4.337086  2.004721e-18  3.137743e-16    12.623492  \n",
      "rab10                   -4.408589  1.780811e-32  1.353823e-29    34.428218  \n",
      "dpagt1                  -4.420954  5.418708e-10  2.074547e-08     4.383914  \n",
      "ceacam1                 -4.455977  1.367349e-26  5.350355e-24    18.356427  \n",
      "fh                      -4.466277  4.102248e-17  5.273073e-15     7.893481  \n",
      "tnw                     -4.531779  1.105582e-12  7.004124e-11     5.887482  \n",
      "crx                     -4.570615  6.873806e-25  2.203593e-22    15.112872  \n",
      "si:ch211-147f12.7       -4.673237  2.477489e-24  7.665236e-22    12.366954  \n",
      "tmem168a                -4.690514  1.603946e-07  3.438983e-06     3.053032  \n",
      "ric8b                   -4.758765  1.030810e-16  1.252410e-14     7.728746  \n",
      "pdha1b                  -4.838514  1.830123e-09  6.227100e-08     3.459056  \n",
      "irf2bp2a                -4.903756  3.107645e-29  1.879278e-26    18.514215  \n",
      "si:ch211-202p1.4        -4.986256  3.915236e-16  4.358854e-14     7.193188  \n",
      "cmn                     -6.342309  2.456732e-29  1.520203e-26    10.458764  \n",
      "\n",
      "[17211 rows x 12 columns]\n"
     ]
    }
   ],
   "source": [
    "print(result)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "df_in_avg = df_in_avg.drop(df_in_avg.index[[0]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "count    17208.000000\n",
      "mean        19.928780\n",
      "std        133.433006\n",
      "min          0.019988\n",
      "25%          1.595746\n",
      "50%          4.854898\n",
      "75%         12.122684\n",
      "max      11006.354410\n",
      "Name: IN_Avg, dtype: float64\n"
     ]
    }
   ],
   "source": [
    "print(df_in_avg.describe())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "cannot concatenate object of type \"<class 'numpy.float64'>\"; only pd.Series, pd.DataFrame, and pd.Panel (deprecated) objs are valid",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-70-8f58dd2de046>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mdataset\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf_in_avg\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mignore_index\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/usr/local/lib/python3.5/dist-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36mappend\u001b[0;34m(self, other, ignore_index, verify_integrity)\u001b[0m\n\u001b[1;32m   5192\u001b[0m             \u001b[0mto_concat\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mother\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   5193\u001b[0m         return concat(to_concat, ignore_index=ignore_index,\n\u001b[0;32m-> 5194\u001b[0;31m                       verify_integrity=verify_integrity)\n\u001b[0m\u001b[1;32m   5195\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   5196\u001b[0m     def join(self, other, on=None, how='left', lsuffix='', rsuffix='',\n",
      "\u001b[0;32m/usr/local/lib/python3.5/dist-packages/pandas/core/reshape/concat.py\u001b[0m in \u001b[0;36mconcat\u001b[0;34m(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, copy)\u001b[0m\n\u001b[1;32m    210\u001b[0m                        \u001b[0mkeys\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlevels\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlevels\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnames\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnames\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    211\u001b[0m                        \u001b[0mverify_integrity\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mverify_integrity\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 212\u001b[0;31m                        copy=copy)\n\u001b[0m\u001b[1;32m    213\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_result\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    214\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python3.5/dist-packages/pandas/core/reshape/concat.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, objs, axis, join, join_axes, keys, levels, names, ignore_index, verify_integrity, copy)\u001b[0m\n\u001b[1;32m    270\u001b[0m                        \u001b[0;34m' only pd.Series, pd.DataFrame, and pd.Panel'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    271\u001b[0m                        ' (deprecated) objs are valid'.format(type(obj)))\n\u001b[0;32m--> 272\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mTypeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    273\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    274\u001b[0m             \u001b[0;31m# consolidate\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mTypeError\u001b[0m: cannot concatenate object of type \"<class 'numpy.float64'>\"; only pd.Series, pd.DataFrame, and pd.Panel (deprecated) objs are valid"
     ]
    }
   ],
   "source": [
    "dataset.append(df_in_avg[1], ignore_index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 146,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['/home/dolley/gear_datasets/Hertzano_Lab/RiboTag_ZF_config.ini']"
      ]
     },
     "execution_count": 146,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import configparser\n",
    "config = configparser.ConfigParser()\n",
    "config.read('/home/dolley/gear_datasets/Hertzano_Lab/RiboTag_ZF_config.ini')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 152,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "average_1\n",
      "average_2\n"
     ]
    }
   ],
   "source": [
    "for col in config['name_average_columns']:\n",
    "    print(col)\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 154,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['IN--1', 'IP--1']\n",
      "IN1_CPM,IN2_CPM,IN3_CPM\n",
      "IP1_CPM,IP2_CPM,IP3_CPM\n"
     ]
    }
   ],
   "source": [
    "avg_col_names = []\n",
    "for col in config['name_average_columns']:\n",
    "    names = avg_col_names.append(config.get('name_average_columns', col))\n",
    "                       \n",
    "print(avg_col_names)\n",
    "        \n",
    "for group in config['replicates']:\n",
    "    columns_string = config.get('replicates', group)\n",
    "    print(columns_string)\n",
    "#     columns = config.get('replicates', group).split(',')\n",
    "#     print(columns)\n",
    "#     col_name = avg_col_names[columns.index(group)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 129,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Gene_name'"
      ]
     },
     "execution_count": 129,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "config['gene_symbol_column']['column_header']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 141,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "awesome\n"
     ]
    }
   ],
   "source": [
    "if config.getboolean('calculations', 'averages') is True:\n",
    "    print('awesome')"
   ]
  }
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