02-lyijin-cov.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[31mlyijin-cov/spis_pH_7.2A.final.annot.cov\u001b[m\u001b[m \u001b[31mlyijin-cov/spis_pH_7.8A.final.annot.cov\u001b[m\u001b[m\n",
      "\u001b[31mlyijin-cov/spis_pH_7.2B.final.annot.cov\u001b[m\u001b[m \u001b[31mlyijin-cov/spis_pH_7.8B.final.annot.cov\u001b[m\u001b[m\n",
      "\u001b[31mlyijin-cov/spis_pH_7.2C.final.annot.cov\u001b[m\u001b[m \u001b[31mlyijin-cov/spis_pH_7.8C.final.annot.cov\u001b[m\u001b[m\n",
      "\u001b[31mlyijin-cov/spis_pH_7.4A.final.annot.cov\u001b[m\u001b[m \u001b[31mlyijin-cov/spis_pH_8.1A.final.annot.cov\u001b[m\u001b[m\n",
      "\u001b[31mlyijin-cov/spis_pH_7.4B.final.annot.cov\u001b[m\u001b[m \u001b[31mlyijin-cov/spis_pH_8.1B.final.annot.cov\u001b[m\u001b[m\n",
      "\u001b[31mlyijin-cov/spis_pH_7.4C.final.annot.cov\u001b[m\u001b[m \u001b[31mlyijin-cov/spis_pH_8.1C.final.annot.cov\u001b[m\u001b[m\n"
     ]
    }
   ],
   "source": [
    "!ls lyijin-cov/*cov"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "==> lyijin-cov/spis_pH_7.2A.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t69.2307692307692\t9\t4\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t81.25\t13\t3\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t20\t3\t12\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t21.0526315789474\t4\t15\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t92.8571428571429\t13\t1\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t81.25\t13\t3\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t57.1428571428571\t8\t6\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t66.6666666666667\t12\t6\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t65\t13\t7\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t72.2222222222222\t13\t5\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.2B.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t69.5652173913043\t16\t7\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t47.0588235294118\t8\t9\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t28.5714285714286\t6\t15\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t23.0769230769231\t6\t20\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t80.9523809523809\t17\t4\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t85.7142857142857\t12\t2\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t45.8333333333333\t11\t13\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t60\t9\t6\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t54.5454545454545\t12\t10\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t66.6666666666667\t12\t6\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.2C.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t76.1904761904762\t16\t5\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t66.6666666666667\t14\t7\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t16.6666666666667\t4\t20\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t16.6666666666667\t3\t15\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t68.1818181818182\t15\t7\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t70.5882352941177\t12\t5\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t42.8571428571429\t9\t12\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t44.4444444444444\t8\t10\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t65\t13\t7\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t73.3333333333333\t11\t4\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.4A.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t75\t15\t5\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t81.8181818181818\t9\t2\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t15.7894736842105\t3\t16\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t22.2222222222222\t4\t14\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t85.7142857142857\t18\t3\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t81.8181818181818\t9\t2\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t54.1666666666667\t13\t11\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t42.8571428571429\t6\t8\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t76.9230769230769\t10\t3\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t100\t11\t0\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.4B.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t77.7777777777778\t14\t4\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t90.4761904761905\t19\t2\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t23.8095238095238\t5\t16\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t18.75\t3\t13\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t38.4615384615385\t5\t8\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t50\t4\t4\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t10\t1\t9\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t20\t2\t8\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t60\t12\t8\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t53.8461538461538\t7\t6\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.4C.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t52.3809523809524\t11\t10\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t53.8461538461538\t7\t6\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t20\t4\t16\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t33.3333333333333\t5\t10\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t82.6086956521739\t19\t4\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t72.7272727272727\t8\t3\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t52.3809523809524\t11\t10\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t53.3333333333333\t8\t7\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t52.1739130434783\t12\t11\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t50\t6\t6\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.8A.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t75\t12\t4\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t69.2307692307692\t9\t4\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t19.047619047619\t4\t17\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t35.7142857142857\t5\t9\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t81.25\t26\t6\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t91.6666666666667\t11\t1\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t36\t9\t16\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t58.3333333333333\t7\t5\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t80\t16\t4\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t75\t12\t4\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.8B.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t58.8235294117647\t10\t7\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t65.5172413793103\t19\t10\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t31.25\t5\t11\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t40\t8\t12\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t92.8571428571429\t13\t1\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t77.7777777777778\t14\t4\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t50\t7\t7\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t63.1578947368421\t12\t7\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t55.5555555555556\t10\t8\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t53.8461538461538\t7\t6\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_7.8C.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t22.2222222222222\t2\t7\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t72.7272727272727\t8\t3\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t40\t4\t6\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t50\t6\t6\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t75\t6\t2\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t92.3076923076923\t12\t1\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t53.3333333333333\t8\t7\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t53.8461538461538\t7\t6\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t71.4285714285714\t15\t6\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t81.8181818181818\t9\t2\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_8.1A.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t57.8947368421053\t11\t8\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t44.4444444444444\t4\t5\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t21.4285714285714\t3\t11\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t33.3333333333333\t2\t4\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t63.6363636363636\t7\t4\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t75\t6\t2\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t40\t4\t6\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t54.5454545454545\t6\t5\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t46.1538461538462\t6\t7\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t60\t9\t6\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_8.1B.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t90\t9\t1\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t50\t7\t7\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t41.6666666666667\t5\t7\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t46.1538461538462\t6\t7\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t84.6153846153846\t11\t2\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t100\t10\t0\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t30.7692307692308\t4\t9\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t30\t3\t7\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t70.5882352941177\t12\t5\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t65\t13\t7\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n",
      "\n",
      "==> lyijin-cov/spis_pH_8.1C.final.annot.cov <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t85.7142857142857\t12\t2\tSpisGene1\t0.17083\t1525\t-7405\tIntron_2_-11\t0.82705\t1030\t-216\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t76.4705882352941\t13\t4\tSpisGene1\t0.17094\t1526\t-7404\tIntron_2_-11\t0.82785\t1031\t-215\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t16.6666666666667\t2\t10\tSpisGene1\t0.17822\t1591\t-7339\tIntron_2_-11\t0.88002\t1096\t-150\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t42.1052631578947\t8\t11\tSpisGene1\t0.17833\t1592\t-7338\tIntron_2_-11\t0.88082\t1097\t-149\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t95.4545454545455\t21\t1\tSpisGene1\t0.19591\t1749\t-7181\tExon_3_-11\t0.068\t8\t-117\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t90\t18\t2\tSpisGene1\t0.19602\t1750\t-7180\tExon_3_-11\t0.076\t9\t-116\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t52.1739130434783\t12\t11\tSpisGene1\t0.20118\t1796\t-7134\tExon_3_-11\t0.444\t55\t-70\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t64.2857142857143\t9\t5\tSpisGene1\t0.20129\t1797\t-7133\tExon_3_-11\t0.452\t56\t-69\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t57.8947368421053\t11\t8\tSpisGene1\t0.21786\t1945\t-6985\tIntron_3_-10\t0.09731\t79\t-738\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t58.3333333333333\t7\t5\tSpisGene1\t0.21797\t1946\t-6984\tIntron_3_-10\t0.09853\t80\t-737\n"
     ]
    }
   ],
   "source": [
    "!head lyijin-cov/*cov"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "Spis.scaffold1|size2969787\n",
      "awk: write error on /dev/stdout\n",
      " input record number 1214, file lyijin-cov/spis_pH_8.1C.final.annot.cov\n",
      " source line number 1\n"
     ]
    }
   ],
   "source": [
    "!awk '{print $1}' lyijin-cov/spis_pH_8.1C.final.annot.cov | head"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!head ../analyses/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/sr320/Documents/GitHub/molecular-prelim/lyijin-cov\n"
     ]
    }
   ],
   "source": [
    "cd lyijin-cov/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "for f in *annot.cov\n",
    "do\n",
    "  STEM=$(basename \"${f}\" .final.annot.cov) \n",
    "  cat \"${f}\" | awk -F $'\\t' 'BEGIN {OFS = FS} {print $1, $2, $3, $4}' \\\n",
    "  > ../analyses/\"${STEM}\".bedgraph\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "==> ../analyses/spis_pH_7.2A.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t69.2307692307692\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t81.25\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t20\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t21.0526315789474\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t92.8571428571429\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t81.25\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t57.1428571428571\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t66.6666666666667\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t65\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t72.2222222222222\n",
      "\n",
      "==> ../analyses/spis_pH_7.2B.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t69.5652173913043\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t47.0588235294118\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t28.5714285714286\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t23.0769230769231\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t80.9523809523809\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t85.7142857142857\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t45.8333333333333\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t60\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t54.5454545454545\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t66.6666666666667\n",
      "\n",
      "==> ../analyses/spis_pH_7.2C.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t76.1904761904762\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t66.6666666666667\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t16.6666666666667\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t16.6666666666667\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t68.1818181818182\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t70.5882352941177\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t42.8571428571429\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t44.4444444444444\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t65\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t73.3333333333333\n",
      "\n",
      "==> ../analyses/spis_pH_7.4A.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t75\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t81.8181818181818\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t15.7894736842105\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t22.2222222222222\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t85.7142857142857\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t81.8181818181818\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t54.1666666666667\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t42.8571428571429\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t76.9230769230769\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t100\n",
      "\n",
      "==> ../analyses/spis_pH_7.4B.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t77.7777777777778\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t90.4761904761905\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t23.8095238095238\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t18.75\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t38.4615384615385\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t50\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t10\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t20\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t60\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t53.8461538461538\n",
      "\n",
      "==> ../analyses/spis_pH_7.4C.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t52.3809523809524\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t53.8461538461538\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t20\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t33.3333333333333\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t82.6086956521739\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t72.7272727272727\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t52.3809523809524\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t53.3333333333333\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t52.1739130434783\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t50\n",
      "\n",
      "==> ../analyses/spis_pH_7.8A.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t75\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t69.2307692307692\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t19.047619047619\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t35.7142857142857\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t81.25\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t91.6666666666667\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t36\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t58.3333333333333\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t80\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t75\n",
      "\n",
      "==> ../analyses/spis_pH_7.8B.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t58.8235294117647\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t65.5172413793103\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t31.25\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t40\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t92.8571428571429\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t77.7777777777778\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t50\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t63.1578947368421\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t55.5555555555556\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t53.8461538461538\n",
      "\n",
      "==> ../analyses/spis_pH_7.8C.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t22.2222222222222\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t72.7272727272727\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t40\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t50\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t75\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t92.3076923076923\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t53.3333333333333\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t53.8461538461538\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t71.4285714285714\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t81.8181818181818\n",
      "\n",
      "==> ../analyses/spis_pH_8.1A.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t57.8947368421053\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t44.4444444444444\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t21.4285714285714\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t33.3333333333333\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t63.6363636363636\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t75\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t40\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t54.5454545454545\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t46.1538461538462\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t60\n",
      "\n",
      "==> ../analyses/spis_pH_8.1B.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t90\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t50\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t41.6666666666667\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t46.1538461538462\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t84.6153846153846\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t100\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t30.7692307692308\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t30\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t70.5882352941177\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t65\n",
      "\n",
      "==> ../analyses/spis_pH_8.1C.bedgraph <==\n",
      "Spis.scaffold1|size2969787\t8660\t8660\t85.7142857142857\n",
      "Spis.scaffold1|size2969787\t8661\t8661\t76.4705882352941\n",
      "Spis.scaffold1|size2969787\t8726\t8726\t16.6666666666667\n",
      "Spis.scaffold1|size2969787\t8727\t8727\t42.1052631578947\n",
      "Spis.scaffold1|size2969787\t8884\t8884\t95.4545454545455\n",
      "Spis.scaffold1|size2969787\t8885\t8885\t90\n",
      "Spis.scaffold1|size2969787\t8931\t8931\t52.1739130434783\n",
      "Spis.scaffold1|size2969787\t8932\t8932\t64.2857142857143\n",
      "Spis.scaffold1|size2969787\t9080\t9080\t57.8947368421053\n",
      "Spis.scaffold1|size2969787\t9081\t9081\t58.3333333333333\n"
     ]
    }
   ],
   "source": [
    "!head ../analyses/*bedgraph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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