analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/Methylpy DMRs vs Methylkit DMRs.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# run call methylation state on .bam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#copy genome and dedup bams to local directory to process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "!scp /Volumes/web/seashell/bu-mox/data/geoduck/v074/Pgenerosa_v074.fa \\\n",
    "/Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Begin flipping the strand of read 2\n",
      "Mon Aug 19 15:37:31 2019\n",
      "\n",
      "[mpileup] 1 samples in 1 input files\n"
     ]
    }
   ],
   "source": [
    "!methylpy call-methylation-state --input-file /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/dedup_bams/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam --paired-end True --path-to-output /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs --sample EPI-205 --ref-fasta /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/Pgenerosa_v074.fa --num-procs 8 --min-cov 3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Begin flipping the strand of read 2\n",
      "Mon Aug 19 16:18:25 2019\n",
      "\n",
      "Input not indexed. Indexing...\n",
      "Mon Aug 19 16:20:20 2019\n",
      "\n",
      "[mpileup] 1 samples in 1 input files\n",
      "Begin flipping the strand of read 2\n",
      "Mon Aug 19 16:35:38 2019\n",
      "\n",
      "[mpileup] 1 samples in 1 input files\n",
      "Begin flipping the strand of read 2\n",
      "Mon Aug 19 16:58:09 2019\n",
      "\n",
      "[mpileup] 1 samples in 1 input files\n"
     ]
    }
   ],
   "source": [
    "!find /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/dedup_bams/*.deduplicated.sorted.bam \\\n",
    "| xargs basename -s .deduplicated.sorted.bam | xargs -I{} methylpy call-methylation-state \\\n",
    "--input-file /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/dedup_bams/{}.deduplicated.sorted.bam \\\n",
    "--paired-end TRUE \\\n",
    "--path-to-output /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs \\\n",
    "--sample {} \\\n",
    "--ref-fasta /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/Pgenerosa_v074.fa \\\n",
    "--num-procs 8 \\\n",
    "--min-cov 3\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# get DMRs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Filtering allc files using 8 node(s).\n",
      "Tue Aug 20 04:56:56 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold1__77_contigs__length_89643857\n",
      "Tue Aug 20 04:58:28 2019\n",
      "\n",
      "Running rms tests for chromosome PGA_scaffold1__77_contigs__length_89643857\n",
      "Tue Aug 20 04:58:30 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold2__36_contigs__length_69596280\n",
      "Tue Aug 20 04:58:30 2019\n",
      "\n",
      "Ran 4848 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_7.tsv\n",
      "Ran 5595 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_1.tsv\n",
      "Ran 5899 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_2.tsv\n",
      "Ran 5154 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_0.tsv\n",
      "Ran 5651 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold2__36_contigs__length_69596280\n",
      "Tue Aug 20 04:58:47 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold3__111_contigs__length_57743597\n",
      "Tue Aug 20 04:58:47 2019\n",
      "\n",
      "Ran 6052 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_5.tsv\n",
      "Ran 5662 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_4.tsv\n",
      "Ran 6033 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_6.tsv\n",
      "Ran 3898 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_2.tsv\n",
      "Ran 3988 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_4.tsv\n",
      "Ran 4303 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_0.tsv\n",
      "Ran 4366 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_3.tsv\n",
      "Ran 3921 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_7.tsv\n",
      "Ran 4170 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_6.tsv\n",
      "Ran 4211 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold3__111_contigs__length_57743597\n",
      "Tue Aug 20 04:59:01 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold4__129_contigs__length_65288255\n",
      "Tue Aug 20 04:59:01 2019\n",
      "\n",
      "Ran 3808 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_1.tsv\n",
      "Ran 2868 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_1.tsv\n",
      "Ran 3020 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_0.tsv\n",
      "Ran 2985 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_6.tsv\n",
      "Ran 3339 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold4__129_contigs__length_65288255\n",
      "Tue Aug 20 04:59:12 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold5__109_contigs__length_67248332\n",
      "Tue Aug 20 04:59:12 2019\n",
      "\n",
      "Ran 3495 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_4.tsv\n",
      "Ran 3671 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_2.tsv\n",
      "Ran 3678 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_5.tsv\n",
      "Ran 3279 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_7.tsv\n",
      "Ran 2858 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_5.tsv\n",
      "Ran 3189 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_0.tsv\n",
      "Ran 3181 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_2.tsv\n",
      "Ran 3572 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold5__109_contigs__length_67248332\n",
      "Tue Aug 20 04:59:22 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold6__104_contigs__length_61759565\n",
      "Tue Aug 20 04:59:22 2019\n",
      "\n",
      "Ran 3428 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_6.tsv\n",
      "Ran 3596 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_4.tsv\n",
      "Ran 3471 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_7.tsv\n",
      "Ran 3767 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_1.tsv\n",
      "Ran 2194 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_0.tsv\n",
      "Ran 2443 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_2.tsv\n",
      "Ran 2706 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_3.tsv\n",
      "Ran 2886 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_4.tsv\n",
      "Running rms tests for chromosome PGA_scaffold6__104_contigs__length_61759565\n",
      "Tue Aug 20 04:59:31 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold7__69_contigs__length_43120122\n",
      "Tue Aug 20 04:59:31 2019\n",
      "\n",
      "Ran 3003 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_1.tsv\n",
      "Ran 3057 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_6.tsv\n",
      "Ran 3357 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_5.tsv\n",
      "Ran 2934 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_7.tsv\n",
      "Ran 2761 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_2.tsv\n",
      "Ran 2951 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_3.tsv\n",
      "Ran 3140 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_4.tsv\n",
      "Ran 2528 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_6.tsv\n",
      "Ran 2957 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold7__69_contigs__length_43120122\n",
      "Tue Aug 20 04:59:41 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold8__63_contigs__length_61151155\n",
      "Tue Aug 20 04:59:41 2019\n",
      "\n",
      "Ran 3018 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_0.tsv\n",
      "Ran 3103 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_7.tsv\n",
      "Ran 2575 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_1.tsv\n",
      "Ran 2119 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_4.tsv\n",
      "Ran 1953 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_2.tsv\n",
      "Ran 2331 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_3.tsv\n",
      "Ran 2684 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_0.tsv\n",
      "Ran 2536 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_1.tsv\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running rms tests for chromosome PGA_scaffold8__63_contigs__length_61151155\n",
      "Tue Aug 20 04:59:48 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold9__45_contigs__length_38581958\n",
      "Tue Aug 20 04:59:48 2019\n",
      "\n",
      "Ran 2512 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_6.tsv\n",
      "Ran 2472 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_5.tsv\n",
      "Ran 1867 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_7.tsv\n",
      "Ran 3191 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_1.tsv\n",
      "Ran 3358 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_2.tsv\n",
      "Ran 3145 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_4.tsv\n",
      "Ran 3030 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_6.tsv\n",
      "Running rms tests for chromosome PGA_scaffold9__45_contigs__length_38581958\n",
      "Tue Aug 20 04:59:58 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold10__49_contigs__length_53961475\n",
      "Tue Aug 20 04:59:58 2019\n",
      "\n",
      "Ran 3548 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_5.tsv\n",
      "Ran 3565 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_3.tsv\n",
      "Ran 2762 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_7.tsv\n",
      "Ran 4142 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_0.tsv\n",
      "Ran 1700 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_2.tsv\n",
      "Ran 2114 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_0.tsv\n",
      "Ran 1815 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_3.tsv\n",
      "Ran 2184 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_4.tsv\n",
      "Ran 2071 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold10__49_contigs__length_53961475\n",
      "Tue Aug 20 05:00:05 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold11__79_contigs__length_51449921\n",
      "Tue Aug 20 05:00:05 2019\n",
      "\n",
      "Ran 2304 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_1.tsv\n",
      "Ran 2017 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_6.tsv\n",
      "Ran 2103 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_7.tsv\n",
      "Ran 2961 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_1.tsv\n",
      "Ran 2933 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_3.tsv\n",
      "Ran 2905 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_0.tsv\n",
      "Ran 2956 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold11__79_contigs__length_51449921\n",
      "Tue Aug 20 05:00:16 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold12__71_contigs__length_50438331\n",
      "Tue Aug 20 05:00:16 2019\n",
      "\n",
      "Ran 3380 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_2.tsv\n",
      "Ran 3184 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_6.tsv\n",
      "Ran 2674 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_7.tsv\n",
      "Ran 3800 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_4.tsv\n",
      "Ran 2075 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_2.tsv\n",
      "Ran 2126 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_3.tsv\n",
      "Ran 2261 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_1.tsv\n",
      "Ran 2302 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_0.tsv\n",
      "Ran 2453 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold12__71_contigs__length_50438331\n",
      "Tue Aug 20 05:00:24 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold13__52_contigs__length_44396874\n",
      "Tue Aug 20 05:00:24 2019\n",
      "\n",
      "Ran 2090 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_7.tsv\n",
      "Ran 2276 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_6.tsv\n",
      "Ran 1799 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_4.tsv\n",
      "Ran 2158 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_2.tsv\n",
      "Ran 2882 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_3.tsv\n",
      "Ran 2801 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_6.tsv\n",
      "Ran 2733 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_0.tsv\n",
      "Running rms tests for chromosome PGA_scaffold13__52_contigs__length_44396874\n",
      "Tue Aug 20 05:00:33 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold14__91_contigs__length_45393038\n",
      "Tue Aug 20 05:00:33 2019\n",
      "\n",
      "Ran 3069 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_5.tsv\n",
      "Ran 2913 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_4.tsv\n",
      "Ran 3011 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_1.tsv\n",
      "Ran 3133 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_7.tsv\n",
      "Ran 1945 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_1.tsv\n",
      "Ran 2346 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_3.tsv\n",
      "Ran 2379 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_2.tsv\n",
      "Ran 2270 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_0.tsv\n",
      "Ran 2222 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_6.tsv\n",
      "Ran 2491 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold14__91_contigs__length_45393038\n",
      "Tue Aug 20 05:00:40 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold15__101_contigs__length_47938513\n",
      "Tue Aug 20 05:00:40 2019\n",
      "\n",
      "Ran 3007 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_4.tsv\n",
      "Ran 1974 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_7.tsv\n",
      "Ran 2831 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_2.tsv\n",
      "Ran 3147 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_0.tsv\n",
      "Ran 3420 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_5.tsv\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running rms tests for chromosome PGA_scaffold15__101_contigs__length_47938513\n",
      "Tue Aug 20 05:00:50 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold16__33_contigs__length_31980953\n",
      "Tue Aug 20 05:00:50 2019\n",
      "\n",
      "Ran 3486 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_3.tsv\n",
      "Ran 2865 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_7.tsv\n",
      "Ran 3375 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_1.tsv\n",
      "Ran 3575 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_4.tsv\n",
      "Ran 3586 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_6.tsv\n",
      "Ran 1833 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_4.tsv\n",
      "Ran 1731 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_2.tsv\n",
      "Ran 1835 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_3.tsv\n",
      "Ran 2049 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_1.tsv\n",
      "Ran 1725 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_0.tsv\n",
      "Running rms tests for chromosome PGA_scaffold16__33_contigs__length_31980953\n",
      "Tue Aug 20 05:00:56 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold17__51_contigs__length_34923512\n",
      "Tue Aug 20 05:00:56 2019\n",
      "\n",
      "Ran 1815 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_6.tsv\n",
      "Ran 2096 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_5.tsv\n",
      "Ran 1772 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_7.tsv\n",
      "Ran 1112 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_1.tsv\n",
      "Ran 1435 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_2.tsv\n",
      "Ran 1545 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_7.tsv\n",
      "Ran 1773 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_3.tsv\n",
      "Ran 1583 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_6.tsv\n",
      "Ran 1535 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold17__51_contigs__length_34923512\n",
      "Tue Aug 20 05:01:02 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold18__69_contigs__length_27737463\n",
      "Tue Aug 20 05:01:02 2019\n",
      "\n",
      "Ran 2230 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_4.tsv\n",
      "Ran 2164 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_0.tsv\n",
      "Ran 1641 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_5.tsv\n",
      "Ran 1828 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_0.tsv\n",
      "Ran 1342 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_7.tsv\n",
      "Running rms tests for chromosome PGA_scaffold18__69_contigs__length_27737463\n",
      "Tue Aug 20 05:01:08 2019\n",
      "\n",
      "Ran 2042 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_4.tsv\n",
      "Ran 2253 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_3.tsv\n",
      "Ran 2182 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_2.tsv\n",
      "Ran 2349 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_1.tsv\n",
      "Ran 2192 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_6.tsv\n",
      "Ran 1067 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_0.tsv\n",
      "Ran 1056 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_1.tsv\n",
      "Ran 1109 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_4.tsv\n",
      "Ran 1258 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_3.tsv\n",
      "Ran 1040 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_5.tsv\n",
      "Ran 852 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_6.tsv\n",
      "Ran 1608 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_2.tsv\n",
      "Ran 1077 root mean square tests. Results in DMR500bp__rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_7.tsv\n",
      "Merging sorted DMR500bp__rms_results.tsv files.\n",
      "Tue Aug 20 05:01:13 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Tue Aug 20 05:01:40 2019\n",
      "\n",
      "m0 estimate for iteration 0: 401015\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Tue Aug 20 05:01:41 2019\n",
      "\n",
      "Begin Defining Windows\n",
      "Tue Aug 20 05:01:49 2019\n",
      "\n",
      "Adding Methylation Levels\n",
      "Tue Aug 20 05:01:55 2019\n",
      "\n",
      "Done\n",
      "Tue Aug 20 05:01:58 2019\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!methylpy DMRfind \\\n",
    "--allc-files  allc_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "--samples EPI-205 EPI-206 EPI-214 EPI-215 EPI-220 EPI-221 EPI-226 EPI-227 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--min-cov 3 \\\n",
    "--output-prefix DMR500bp_ \\\n",
    "--dmr-max-dist 1000 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 1 1 1 1 0 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "#call DMS within a 25 bp window"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Filtering allc files using 8 node(s).\n",
      "Tue Aug 20 06:25:44 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold1__77_contigs__length_89643857\n",
      "Tue Aug 20 06:27:16 2019\n",
      "\n",
      "Running rms tests for chromosome PGA_scaffold1__77_contigs__length_89643857\n",
      "Tue Aug 20 06:27:19 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold2__36_contigs__length_69596280\n",
      "Tue Aug 20 06:27:19 2019\n",
      "\n",
      "Ran 7154 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_7.tsv\n",
      "Ran 7962 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_2.tsv\n",
      "Ran 7796 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_1.tsv\n",
      "Ran 7321 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_0.tsv\n",
      "Ran 7873 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold2__36_contigs__length_69596280\n",
      "Tue Aug 20 06:27:49 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold3__111_contigs__length_57743597\n",
      "Tue Aug 20 06:27:49 2019\n",
      "\n",
      "Ran 8266 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_6.tsv\n",
      "Ran 8316 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_5.tsv\n",
      "Ran 7959 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold1__77_contigs__length_89643857_chunk_4.tsv\n",
      "Ran 5876 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_3.tsv\n",
      "Ran 5635 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_4.tsv\n",
      "Ran 5470 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_2.tsv\n",
      "Ran 5774 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_0.tsv\n",
      "Running rms tests for chromosome PGA_scaffold3__111_contigs__length_57743597\n",
      "Tue Aug 20 06:28:12 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold4__129_contigs__length_65288255\n",
      "Tue Aug 20 06:28:12 2019\n",
      "\n",
      "Ran 5944 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_6.tsv\n",
      "Ran 5893 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_5.tsv\n",
      "Ran 5577 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_7.tsv\n",
      "Ran 4200 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_1.tsv\n",
      "Ran 4248 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_0.tsv\n",
      "Ran 4969 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_2.tsv\n",
      "Ran 4230 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_6.tsv\n",
      "Running rms tests for chromosome PGA_scaffold4__129_contigs__length_65288255\n",
      "Tue Aug 20 06:28:33 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold5__109_contigs__length_67248332\n",
      "Tue Aug 20 06:28:33 2019\n",
      "\n",
      "Ran 5008 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_5.tsv\n",
      "Ran 4589 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_3.tsv\n",
      "Ran 4805 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_4.tsv\n",
      "Ran 4547 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold3__111_contigs__length_57743597_chunk_7.tsv\n",
      "Ran 4592 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_2.tsv\n",
      "Ran 4424 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_0.tsv\n",
      "Ran 5015 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_3.tsv\n",
      "Ran 4303 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_5.tsv\n",
      "Running rms tests for chromosome PGA_scaffold5__109_contigs__length_67248332\n",
      "Tue Aug 20 06:28:54 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold6__104_contigs__length_61759565\n",
      "Tue Aug 20 06:28:54 2019\n",
      "\n",
      "Ran 5065 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_4.tsv\n",
      "Ran 5241 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_1.tsv\n",
      "Ran 4777 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_6.tsv\n",
      "Ran 3669 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_2.tsv\n",
      "Ran 3265 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_0.tsv\n",
      "Ran 3967 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_3.tsv\n",
      "Ran 3990 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_4.tsv\n",
      "Ran 4082 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_1.tsv\n",
      "Running rms tests for chromosome PGA_scaffold6__104_contigs__length_61759565\n",
      "Tue Aug 20 06:29:14 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold7__69_contigs__length_43120122\n",
      "Tue Aug 20 06:29:14 2019\n",
      "\n",
      "Ran 4810 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold4__129_contigs__length_65288255_chunk_7.tsv\n",
      "Ran 4072 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_7.tsv\n",
      "Ran 4108 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_6.tsv\n",
      "Ran 4537 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold5__109_contigs__length_67248332_chunk_5.tsv\n",
      "Ran 4031 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_2.tsv\n",
      "Ran 5302 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold2__36_contigs__length_69596280_chunk_1.tsv\n",
      "Ran 4392 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_0.tsv\n",
      "Ran 4120 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold7__69_contigs__length_43120122\n",
      "Tue Aug 20 06:29:34 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold8__63_contigs__length_61151155\n",
      "Tue Aug 20 06:29:34 2019\n",
      "\n",
      "Ran 4397 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_4.tsv\n",
      "Ran 4133 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_5.tsv\n",
      "Ran 3675 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_6.tsv\n",
      "Ran 4286 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_7.tsv\n",
      "Ran 2869 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_2.tsv\n",
      "Ran 3490 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_1.tsv\n",
      "Ran 3609 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_0.tsv\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running rms tests for chromosome PGA_scaffold8__63_contigs__length_61151155\n",
      "Tue Aug 20 06:29:51 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold9__45_contigs__length_38581958\n",
      "Tue Aug 20 06:29:51 2019\n",
      "\n",
      "Ran 3035 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_4.tsv\n",
      "Ran 3341 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_3.tsv\n",
      "Ran 2792 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_7.tsv\n",
      "Ran 3422 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_5.tsv\n",
      "Ran 3480 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold7__69_contigs__length_43120122_chunk_6.tsv\n",
      "Ran 4541 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_1.tsv\n",
      "Ran 4761 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_2.tsv\n",
      "Running rms tests for chromosome PGA_scaffold9__45_contigs__length_38581958\n",
      "Tue Aug 20 06:30:12 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold10__49_contigs__length_53961475\n",
      "Tue Aug 20 06:30:12 2019\n",
      "\n",
      "Ran 4422 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_6.tsv\n",
      "Ran 4473 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_4.tsv\n",
      "Ran 4861 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_3.tsv\n",
      "Ran 5579 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_0.tsv\n",
      "Ran 4996 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_5.tsv\n",
      "Ran 2888 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_0.tsv\n",
      "Ran 2416 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_2.tsv\n",
      "Ran 2974 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_4.tsv\n",
      "Ran 2610 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_3.tsv\n",
      "Ran 2912 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_5.tsv\n",
      "Ran 3910 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold8__63_contigs__length_61151155_chunk_7.tsv\n",
      "Running rms tests for chromosome PGA_scaffold10__49_contigs__length_53961475\n",
      "Tue Aug 20 06:30:27 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold11__79_contigs__length_51449921\n",
      "Tue Aug 20 06:30:27 2019\n",
      "\n",
      "Ran 2876 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_6.tsv\n",
      "Ran 3095 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_1.tsv\n",
      "Ran 2835 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold9__45_contigs__length_38581958_chunk_7.tsv\n",
      "Ran 4183 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_1.tsv\n",
      "Ran 4130 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_3.tsv\n",
      "Ran 4048 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_0.tsv\n",
      "Ran 4719 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_2.tsv\n",
      "Running rms tests for chromosome PGA_scaffold11__79_contigs__length_51449921\n",
      "Tue Aug 20 06:30:45 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold12__71_contigs__length_50438331\n",
      "Tue Aug 20 06:30:45 2019\n",
      "\n",
      "Ran 4068 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_5.tsv\n",
      "Ran 4291 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_6.tsv\n",
      "Ran 5096 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_4.tsv\n",
      "Ran 3079 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_2.tsv\n",
      "Ran 3289 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_0.tsv\n",
      "Ran 3698 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold10__49_contigs__length_53961475_chunk_7.tsv\n",
      "Ran 3248 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_1.tsv\n",
      "Running rms tests for chromosome PGA_scaffold12__71_contigs__length_50438331\n",
      "Tue Aug 20 06:31:01 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold13__52_contigs__length_44396874\n",
      "Tue Aug 20 06:31:01 2019\n",
      "\n",
      "Ran 3062 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_3.tsv\n",
      "Ran 3351 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_5.tsv\n",
      "Ran 3062 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_7.tsv\n",
      "Ran 3246 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_6.tsv\n",
      "Ran 3153 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_2.tsv\n",
      "Ran 3783 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold6__104_contigs__length_61759565_chunk_1.tsv\n",
      "Ran 3788 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_0.tsv\n",
      "Ran 4147 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_1.tsv\n",
      "Running rms tests for chromosome PGA_scaffold13__52_contigs__length_44396874\n",
      "Tue Aug 20 06:31:18 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold14__91_contigs__length_45393038\n",
      "Tue Aug 20 06:31:18 2019\n",
      "\n",
      "Ran 4066 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_3.tsv\n",
      "Ran 4367 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_5.tsv\n",
      "Ran 4148 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_4.tsv\n",
      "Ran 3925 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_6.tsv\n",
      "Ran 4285 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold12__71_contigs__length_50438331_chunk_7.tsv\n",
      "Ran 2906 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_1.tsv\n",
      "Ran 3286 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_0.tsv\n",
      "Ran 3281 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_2.tsv\n",
      "Ran 3132 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold14__91_contigs__length_45393038\n",
      "Tue Aug 20 06:31:35 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold15__101_contigs__length_47938513\n",
      "Tue Aug 20 06:31:35 2019\n",
      "\n",
      "Ran 3382 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_5.tsv\n",
      "Ran 4068 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_4.tsv\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Ran 3244 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_6.tsv\n",
      "Ran 2892 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold13__52_contigs__length_44396874_chunk_7.tsv\n",
      "Ran 4158 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_2.tsv\n",
      "Ran 4694 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_0.tsv\n",
      "Running rms tests for chromosome PGA_scaffold15__101_contigs__length_47938513\n",
      "Tue Aug 20 06:31:56 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold16__33_contigs__length_31980953\n",
      "Tue Aug 20 06:31:56 2019\n",
      "\n",
      "Ran 4797 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_3.tsv\n",
      "Ran 4901 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_5.tsv\n",
      "Ran 4773 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_1.tsv\n",
      "Ran 4997 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_4.tsv\n",
      "Ran 5002 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_6.tsv\n",
      "Ran 4224 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold14__91_contigs__length_45393038_chunk_7.tsv\n",
      "Ran 2764 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_3.tsv\n",
      "Ran 2893 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_1.tsv\n",
      "Ran 2669 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_2.tsv\n",
      "Ran 2715 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_4.tsv\n",
      "Ran 2524 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_0.tsv\n",
      "Running rms tests for chromosome PGA_scaffold16__33_contigs__length_31980953\n",
      "Tue Aug 20 06:32:12 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold17__51_contigs__length_34923512\n",
      "Tue Aug 20 06:32:12 2019\n",
      "\n",
      "Ran 2587 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold11__79_contigs__length_51449921_chunk_4.tsv\n",
      "Ran 3066 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_5.tsv\n",
      "Ran 1803 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_1.tsv\n",
      "Ran 2618 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_7.tsv\n",
      "Ran 2733 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold15__101_contigs__length_47938513_chunk_6.tsv\n",
      "Ran 2588 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_3.tsv\n",
      "Running rms tests for chromosome PGA_scaffold17__51_contigs__length_34923512\n",
      "Tue Aug 20 06:32:22 2019\n",
      "\n",
      "Splitting allc files for chromosome PGA_scaffold18__69_contigs__length_27737463\n",
      "Tue Aug 20 06:32:22 2019\n",
      "\n",
      "Ran 2168 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_2.tsv\n",
      "Ran 2328 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_5.tsv\n",
      "Ran 2885 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_4.tsv\n",
      "Ran 2329 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_7.tsv\n",
      "Ran 2341 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_6.tsv\n",
      "Ran 2941 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold16__33_contigs__length_31980953_chunk_0.tsv\n",
      "Ran 2716 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_0.tsv\n",
      "Running rms tests for chromosome PGA_scaffold18__69_contigs__length_27737463\n",
      "Tue Aug 20 06:32:36 2019\n",
      "\n",
      "Ran 2468 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_5.tsv\n",
      "Ran 3209 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_3.tsv\n",
      "Ran 3392 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_1.tsv\n",
      "Ran 3062 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_2.tsv\n",
      "Ran 3048 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_6.tsv\n",
      "Ran 2934 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_4.tsv\n",
      "Ran 2265 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold17__51_contigs__length_34923512_chunk_7.tsv\n",
      "Ran 1665 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_0.tsv\n",
      "Ran 1670 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_4.tsv\n",
      "Ran 1629 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_1.tsv\n",
      "Ran 1325 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_6.tsv\n",
      "Ran 1806 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_7.tsv\n",
      "Ran 1921 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_3.tsv\n",
      "Ran 1690 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_5.tsv\n",
      "Ran 2200 root mean square tests. Results in DMR1000bpMCmax25_rms_results_for_PGA_scaffold18__69_contigs__length_27737463_chunk_2.tsv\n",
      "Merging sorted DMR1000bpMCmax25_rms_results.tsv files.\n",
      "Tue Aug 20 06:32:46 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Tue Aug 20 06:33:23 2019\n",
      "\n",
      "m0 estimate for iteration 0: 566773\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Tue Aug 20 06:33:25 2019\n",
      "\n",
      "Begin Defining Windows\n",
      "Tue Aug 20 06:33:35 2019\n",
      "\n",
      "Adding Methylation Levels\n",
      "Tue Aug 20 06:33:45 2019\n",
      "\n",
      "Done\n",
      "Tue Aug 20 06:33:54 2019\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!methylpy DMRfind \\\n",
    "--allc-files  allc_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "allc_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "--samples EPI-205 EPI-206 EPI-214 EPI-215 EPI-220 EPI-221 EPI-226 EPI-227 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--min-cov 3 \\\n",
    "--output-prefix DMR1000bpMCmax25 \\\n",
    "--mc-max-dist 25 \\\n",
    "--dmr-max-dist 1000 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 1 1 1 1 0 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create bigwig file\n",
    "#HAD TO INSTALL WIGTOBIGWIG SOFTWARE\n",
    "#https://bioconda.github.io/recipes/ucsc-wigtobigwig/README.html\n",
    "#first had to set my conda channels in the correct order\n",
    "## ``` \n",
    "## conda config --add channels defaults\n",
    "## conda config --add channels bioconda\n",
    "## conda config --add channels conda-forge\n",
    "## ```\n",
    "#then install the sofware\n",
    "## ```\n",
    "## conda install ucsc-wigtobigwig\n",
    "## ```\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "!find /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/*_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "| xargs basename -s _L004_R1_001_val_1_bismark_bt2_pe.tsv.gz | xargs -I{} methylpy allc-to-bigwig \\\n",
    "--allc-file {}_L004_R1_001_val_1_bismark_bt2_pe.tsv.gz \\\n",
    "--output-file {}.bw \\\n",
    "--ref-fasta /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/Pgenerosa_v074.fa \\\n",
    "--mc-type CGN \\\n",
    "--bin-size 250"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "chrPGA_scaffold10__49_contigs__length_53961475\t24714286\t24714301\t4\r\n",
      "chrPGA_scaffold11__79_contigs__length_51449921\t1542753\t1542811\t3\r\n",
      "chrPGA_scaffold11__79_contigs__length_51449921\t41762167\t41762215\t5\r\n",
      "chrPGA_scaffold11__79_contigs__length_51449921\t46692952\t46692987\t3\r\n",
      "chrPGA_scaffold13__52_contigs__length_44396874\t12130155\t12130180\t3\r\n",
      "chrPGA_scaffold13__52_contigs__length_44396874\t17574534\t17574550\t3\r\n",
      "chrPGA_scaffold14__91_contigs__length_45393038\t7707795\t7707940\t8\r\n",
      "chrPGA_scaffold14__91_contigs__length_45393038\t7715685\t7715988\t3\r\n",
      "chrPGA_scaffold15__101_contigs__length_47938513\t5533042\t5533096\t10\r\n",
      "chrPGA_scaffold15__101_contigs__length_47938513\t18905757\t18905806\t7\r\n"
     ]
    }
   ],
   "source": [
    "!head DMR1000bpMCmax25_rms_results_collapsed.tsv.DMR.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#chr\tstart\tend\tnumber_of_dms\thypermethylated_samples\thypomethylated_samples\tmethylation_level_EPI-205\tmethylation_level_EPI-206\tmethylation_level_EPI-214\tmethylation_level_EPI-215\tmethylation_level_EPI-220\tmethylation_level_EPI-221\tmethylation_level_EPI-226\tmethylation_level_EPI-227\r\n",
      "PGA_scaffold10__49_contigs__length_53961475\t24714287\t24714301\t4\tEPI-206,EPI-226,EPI-227\tEPI-214,EPI-215\t0.6666666666666666\t0.9444444444444444\t0.25806451612903225\t0.3333333333333333\t0.36363636363636365\t0.6666666666666666\t1.0\t1.0\r\n",
      "PGA_scaffold11__79_contigs__length_51449921\t1542754\t1542811\t3\tEPI-215,EPI-220\tEPI-226,EPI-205\t0.36363636363636365\t0.8333333333333334\tNA\t1.0\t1.0\tNA\t0.15789473684210525\t0.75\r\n",
      "PGA_scaffold11__79_contigs__length_51449921\t41762168\t41762215\t5\tEPI-215,EPI-220\tEPI-206\tNA\t0.0967741935483871\t0.5333333333333333\t1.0\t0.8333333333333334\t0.45454545454545453\t0.3333333333333333\t0.3333333333333333\r\n",
      "PGA_scaffold11__79_contigs__length_51449921\t46692953\t46692987\t3\tEPI-215,EPI-221\tEPI-206\t0.3333333333333333\t0.0625\t0.0\t1.0\tNA\t1.0\t0.16666666666666666\tNA\r\n",
      "PGA_scaffold13__52_contigs__length_44396874\t12130156\t12130180\t3\tEPI-205,EPI-226\tEPI-214,EPI-220\t0.6666666666666666\t0.45454545454545453\t0.0\t0.16666666666666666\t0.0\t0.4\t0.5714285714285714\t0.3333333333333333\r\n",
      "PGA_scaffold13__52_contigs__length_44396874\t17574535\t17574550\t3\tEPI-220,EPI-215\tEPI-206\tNA\t0.0\tNA\t0.6875\t1.0\tNA\tNA\tNA\r\n",
      "PGA_scaffold14__91_contigs__length_45393038\t7707796\t7707940\t8\tEPI-214,EPI-215\tEPI-206\t0.6216216216216216\t0.034482758620689655\t0.8805970149253731\t0.9384615384615385\t0.6818181818181818\t0.75\tNA\tNA\r\n",
      "PGA_scaffold14__91_contigs__length_45393038\t7715686\t7715988\t3\tEPI-214,EPI-215\tEPI-205\t0.59375\t0.0\t0.8842105263157894\t0.9285714285714286\t0.625\t0.23809523809523808\tNA\t1.0\r\n",
      "PGA_scaffold15__101_contigs__length_47938513\t5533043\t5533096\t10\tEPI-205,EPI-227\tEPI-221\t0.75\t0.5158371040723982\t0.5429447852760736\t0.5737704918032787\t0.5397727272727273\t0.42342342342342343\t0.656\t0.6946564885496184\r\n"
     ]
    }
   ],
   "source": [
    "!head DMR1000bpMCmax25_rms_results_collapsed.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "chrPGA_scaffold10__49_contigs__length_53961475\t526\t527\tCGG;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t708\t709\tCGC;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t731\t732\tCGG;+\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t732\t733\tCGA;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t734\t735\tCGA;+\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t735\t736\tCGC;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t742\t743\tCGG;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t758\t759\tCGA;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t764\t765\tCGG;-\t0.0003\r\n",
      "chrPGA_scaffold10__49_contigs__length_53961475\t892\t893\tCGT;-\t0.0003\r\n"
     ]
    }
   ],
   "source": [
    "!head DMR1000bpMCmax25_rms_results_collapsed.tsv.DMS.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#create bedgraphs from coverage files showing these DMRs so I can confirm DMRs are realistic in IGV"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Volumes/web/seashell/bu-mox/scrubbed/0807-004\n"
     ]
    }
   ],
   "source": [
    "cd /Volumes/web/seashell/bu-mox/scrubbed/0807-004"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t6002\t6004\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t6002\t6004\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t53\t55\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t53\t55\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t6002\t6004\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t6002\t6004\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t2508\t2510\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t2508\t2510\t0\t0\t4\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3070\t3072\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3070\t3072\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3002\t3004\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3002\t3004\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t6002\t6004\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t6002\t6004\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t3722\t3724\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t2508\t2510\t0\t0\t3\n",
      "\n",
      "***** WARNING: File - has inconsistent naming convention for record:\n",
      "PGA_scaffold1__77_contigs__length_89643857\t2508\t2510\t0\t0\t3\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "for f in *.cov.gz\n",
    "do\n",
    "zcat < ${f} | awk '{if($5+$6 >=3)print $0}'| /Users/Shared/bioinformatics/bedtools2/bin/intersectBed -a - -b /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/DMR1000bpMCmax25_rms_results_collapsed.tsv.DMR.bed | awk -F\"\\t\" '{print $1FS$2FS$3FS$4FS$5+$6}' > /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/${f}.3xcov.DMR.bedgraph\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "chrPGA_scaffold10__49_contigs__length_53961475\t24714286\t24714301\t4\r\n",
      "chrPGA_scaffold11__79_contigs__length_51449921\t1542753\t1542811\t3\r\n",
      "chrPGA_scaffold11__79_contigs__length_51449921\t41762167\t41762215\t5\r\n",
      "chrPGA_scaffold11__79_contigs__length_51449921\t46692952\t46692987\t3\r\n",
      "chrPGA_scaffold13__52_contigs__length_44396874\t12130155\t12130180\t3\r\n",
      "chrPGA_scaffold13__52_contigs__length_44396874\t17574534\t17574550\t3\r\n",
      "chrPGA_scaffold14__91_contigs__length_45393038\t7707795\t7707940\t8\r\n",
      "chrPGA_scaffold14__91_contigs__length_45393038\t7715685\t7715988\t3\r\n",
      "chrPGA_scaffold15__101_contigs__length_47938513\t5533042\t5533096\t10\r\n",
      "chrPGA_scaffold15__101_contigs__length_47938513\t18905757\t18905806\t7\r\n"
     ]
    }
   ],
   "source": [
    "!head /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/DMR1000bpMCmax25_rms_results_collapsed.tsv.DMR.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#need to remov chr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "sed 's/chr//g' /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/DMR1000bpMCmax25_rms_results_collapsed.tsv.DMR.bed > /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/DMR1000bpMCmax25_rms_results_collapsed.tsv.DMRnochr.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#now try to create bedgraph files again"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "for f in *.cov.gz\n",
    "do\n",
    "zcat < ${f} | awk '{if($5+$6 >=3)print $0}'| /Users/Shared/bioinformatics/bedtools2/bin/intersectBed -a - -b /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/DMR1000bpMCmax25_rms_results_collapsed.tsv.DMRnochr.bed | awk -F\"\\t\" '{print $1FS$2FS$3FS$4FS$5+$6}' > /Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_SR_v074_alignments/methylpy_DMRs/${f}.3xcov.DMR.bedgraph\n",
    "done"
   ]
  }
 ],
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    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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