jupyter/CreatePromoterTrackAnd250bpBinTrack.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#create promoter track"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#first copy genome data and gff locally"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/strigg/Documents/GitHub/Salmon_sealice/data\n"
     ]
    }
   ],
   "source": [
    "cd ~/Documents/GitHub/Salmon_sealice/data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GCF_000233375.1_ICSASG_v2_genomic.fa.fai\n",
      "        1489 100%    0.00kB/s    0:00:00 (xfer#1, to-check=0/1)\n",
      "\n",
      "sent 1610 bytes  received 42 bytes  3304.00 bytes/sec\n",
      "total size is 1489  speedup is 0.90\n"
     ]
    }
   ],
   "source": [
    "!rsync --progress --verbose /Volumes/web/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa.fai ."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ref_ICSASG_v2_top_level.gff3.gz\n",
      "    37706696 100%   37.62MB/s    0:00:00 (xfer#1, to-check=0/1)\n",
      "\n",
      "sent 37711408 bytes  received 42 bytes  25140966.67 bytes/sec\n",
      "total size is 37706696  speedup is 1.00\n"
     ]
    }
   ],
   "source": [
    "!rsync --progress --verbose /Volumes/web/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq/ref_ICSASG_v2_top_level.gff3.gz ."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#unzip gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "!gunzip ref_ICSASG_v2_top_level.gff3.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#create gene gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "cat ref_ICSASG_v2_top_level.gff3 |\\\n",
    "awk '{if($3 == \"gene\")print $0}' > ref_ICSASG_v2_top_level.gene.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#preview gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tgene\t5501\t62139\t.\t-\t.\tID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tgene\t160437\t198815\t.\t-\t.\tID=gene1;Dbxref=GeneID:106607996;Name=LOC106607996;gbkey=Gene;gene=LOC106607996;gene_biotype=protein_coding;partial=true;start_range=.,160437\r\n",
      "NC_027300.1\tGnomon\tgene\t228330\t231471\t.\t-\t.\tID=gene2;Dbxref=GeneID:106601976;Name=LOC106601976;end_range=231471,.;gbkey=Gene;gene=LOC106601976;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tgene\t296031\t297111\t.\t-\t.\tID=gene3;Dbxref=GeneID:106560213;Name=LOC106560213;gbkey=Gene;gene=LOC106560213;gene_biotype=protein_coding;partial=true;start_range=.,296031\r\n",
      "NC_027300.1\tGnomon\tgene\t306942\t310878\t.\t+\t.\tID=gene4;Dbxref=GeneID:106566220;Name=LOC106566220;gbkey=Gene;gene=LOC106566220;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tgene\t331369\t346454\t.\t-\t.\tID=gene5;Dbxref=GeneID:106571988;Name=LOC106571988;end_range=346454,.;gbkey=Gene;gene=LOC106571988;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tgene\t355675\t362950\t.\t+\t.\tID=gene6;Dbxref=GeneID:106578259;Name=LOC106578259;end_range=362950,.;gbkey=Gene;gene=LOC106578259;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tgene\t401623\t416794\t.\t+\t.\tID=gene7;Dbxref=GeneID:106583877;Name=LOC106583877;gbkey=Gene;gene=LOC106583877;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tgene\t431662\t432555\t.\t-\t.\tID=gene8;Dbxref=GeneID:106589664;Name=LOC106589664;gbkey=Gene;gene=LOC106589664;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tgene\t449112\t490663\t.\t+\t.\tID=gene9;Dbxref=GeneID:106596642;Name=LOC106596642;end_range=490663,.;gbkey=Gene;gene=LOC106596642;gene_biotype=protein_coding;partial=true\r\n"
     ]
    }
   ],
   "source": [
    "!head ref_ICSASG_v2_top_level.gene.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#preview chromosomes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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    {
     "name": "stdout",
     "output_type": "stream",
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    {
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      "   3 NW_012570814.1\r\n",
      "   1 NW_012570882.1\r\n",
      "   1 NW_012570921.1\r\n",
      "   2 NW_012570936.1\r\n",
      "   1 NW_012570938.1\r\n",
      "   1 NW_012570967.1\r\n",
      "   1 NW_012570971.1\r\n",
      "   1 NW_012570999.1\r\n",
      "   1 NW_012571003.1\r\n",
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      "   1 NW_012571035.1\r\n",
      "   2 NW_012571057.1\r\n",
      "   1 NW_012571088.1\r\n",
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      "   1 NW_012571163.1\r\n",
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      "   1 NW_012571268.1\r\n",
      "   2 NW_012571277.1\r\n",
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      "   1 NW_012571359.1\r\n",
      "   1 NW_012571386.1\r\n",
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      "   1 NW_012571599.1\r\n",
      "   2 NW_012571604.1\r\n",
      "   1 NW_012571628.1\r\n",
      "   2 NW_012571631.1\r\n",
      "   1 NW_012571650.1\r\n",
      "   1 NW_012571651.1\r\n",
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      "   1 NW_012571709.1\r\n",
      "   1 NW_012571792.1\r\n",
      "   1 NW_012571821.1\r\n",
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      "   1 NW_012571848.1\r\n",
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      "   1 NW_012571873.1\r\n",
      "   2 NW_012571875.1\r\n",
      "   1 NW_012571894.1\r\n",
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      "   1 NW_012571972.1\r\n",
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      "   1 NW_012572017.1\r\n",
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      "   1 NW_012572110.1\r\n",
      "   1 NW_012572132.1\r\n",
      "   1 NW_012572195.1\r\n",
      "   1 NW_012572205.1\r\n",
      "   2 NW_012572213.1\r\n",
      "   1 NW_012572215.1\r\n",
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      "   2 NW_012572304.1\r\n",
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      "   1 NW_012572788.1\r\n",
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      "   1 NW_012572865.1\r\n",
      "   1 NW_012572916.1\r\n",
      "   1 NW_012572921.1\r\n",
      "   1 NW_012572931.1\r\n",
      "   2 NW_012573015.1\r\n",
      "   1 NW_012573039.1\r\n",
      "   1 NW_012573047.1\r\n",
      "   2 NW_012573088.1\r\n",
      "   1 NW_012573093.1\r\n",
      "   2 NW_012573099.1\r\n",
      "   2 NW_012573133.1\r\n",
      "   1 NW_012573138.1\r\n",
      "   1 NW_012573156.1\r\n",
      "   1 NW_012573157.1\r\n",
      "   1 NW_012573166.1\r\n",
      "   1 NW_012573173.1\r\n",
      "   2 NW_012573181.1\r\n",
      "   1 NW_012573182.1\r\n",
      "   1 NW_012573184.1\r\n",
      "   1 NW_012573189.1\r\n",
      "   1 NW_012573239.1\r\n",
      "   1 NW_012573284.1\r\n",
      "   1 NW_012573313.1\r\n",
      "   1 NW_012573355.1\r\n",
      "   2 NW_012573369.1\r\n",
      "   1 NW_012573378.1\r\n",
      "   1 NW_012573379.1\r\n",
      "   1 NW_012573400.1\r\n",
      "   3 NW_012573417.1\r\n",
      "   1 NW_012573437.1\r\n",
      "   1 NW_012573473.1\r\n",
      "   1 NW_012573477.1\r\n",
      "   1 NW_012573480.1\r\n",
      "   1 NW_012573565.1\r\n",
      "   1 NW_012573568.1\r\n",
      "   1 NW_012573575.1\r\n",
      "   2 NW_012573577.1\r\n",
      "   2 NW_012573626.1\r\n",
      "   2 NW_012573695.1\r\n",
      "   1 NW_012573701.1\r\n",
      "   2 NW_012573752.1\r\n",
      "   2 NW_012573819.1\r\n",
      "   2 NW_012573846.1\r\n",
      "   1 NW_012573861.1\r\n",
      "   1 NW_012573932.1\r\n",
      "   1 NW_012573936.1\r\n",
      "   1 NW_012573956.1\r\n",
      "   2 NW_012573963.1\r\n",
      "   1 NW_012573988.1\r\n",
      "   2 NW_012574000.1\r\n",
      "   1 NW_012574031.1\r\n",
      "   2 NW_012574040.1\r\n",
      "   1 NW_012574052.1\r\n",
      "   1 NW_012574062.1\r\n",
      "   1 NW_012574098.1\r\n",
      "   2 NW_012574160.1\r\n",
      "   1 NW_012574198.1\r\n",
      "   1 NW_012574205.1\r\n",
      "   2 NW_012574247.1\r\n",
      "   1 NW_012574275.1\r\n",
      "   2 NW_012574348.1\r\n",
      "   1 NW_012574355.1\r\n",
      "   1 NW_012574369.1\r\n"
     ]
    }
   ],
   "source": [
    "!cat ref_ICSASG_v2_top_level.gene.gff3 |\\\n",
    "awk -F\"\\t\" '{if($0!~/#/)print $1}' |\\\n",
    "sort | \\\n",
    "uniq -c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#remove NW sequences"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  13 NC_001960.1\n",
      "3189 NC_027300.1\n",
      "2451 NC_027301.1\n",
      "2811 NC_027302.1\n",
      "2188 NC_027303.1\n",
      "2201 NC_027304.1\n",
      "2370 NC_027305.1\n",
      "1569 NC_027306.1\n",
      " 744 NC_027307.1\n",
      "2899 NC_027308.1\n",
      "2286 NC_027309.1\n",
      "2130 NC_027310.1\n",
      "2497 NC_027311.1\n",
      "2357 NC_027312.1\n",
      "2245 NC_027313.1\n",
      "2222 NC_027314.1\n",
      "1974 NC_027315.1\n",
      "1633 NC_027316.1\n",
      "1579 NC_027317.1\n",
      "1548 NC_027318.1\n",
      "1877 NC_027319.1\n",
      " 993 NC_027320.1\n",
      "1349 NC_027321.1\n",
      "1036 NC_027322.1\n",
      "1114 NC_027323.1\n",
      " 947 NC_027324.1\n",
      "1389 NC_027325.1\n",
      "1142 NC_027326.1\n",
      " 833 NC_027327.1\n",
      " 687 NC_027328.1\n"
     ]
    }
   ],
   "source": [
    "!cat ref_ICSASG_v2_top_level.gene.gff3 |\\\n",
    "awk -F\"\\t\" '{if($0!~/NW_/)print $1}' |\\\n",
    "sort |\\\n",
    "uniq -c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "!cat ref_ICSASG_v2_top_level.gene.gff3 |\\\n",
    "awk -F\"\\t\" '{if($0!~/NW_/)print $0}' \\\n",
    "> ref_ICSASG_v2_top_level.gene.noNW.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#create promoter track"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tgene\t62140\t64639\t.\t-\t.\tID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tgene\t198816\t201315\t.\t-\t.\tID=gene1;Dbxref=GeneID:106607996;Name=LOC106607996;gbkey=Gene;gene=LOC106607996;gene_biotype=protein_coding;partial=true;start_range=.,160437\n",
      "NC_027300.1\tGnomon\tgene\t231472\t233971\t.\t-\t.\tID=gene2;Dbxref=GeneID:106601976;Name=LOC106601976;end_range=231471,.;gbkey=Gene;gene=LOC106601976;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tgene\t297112\t299611\t.\t-\t.\tID=gene3;Dbxref=GeneID:106560213;Name=LOC106560213;gbkey=Gene;gene=LOC106560213;gene_biotype=protein_coding;partial=true;start_range=.,296031\n",
      "NC_027300.1\tGnomon\tgene\t304442\t306941\t.\t+\t.\tID=gene4;Dbxref=GeneID:106566220;Name=LOC106566220;gbkey=Gene;gene=LOC106566220;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tgene\t346455\t348954\t.\t-\t.\tID=gene5;Dbxref=GeneID:106571988;Name=LOC106571988;end_range=346454,.;gbkey=Gene;gene=LOC106571988;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tgene\t353175\t355674\t.\t+\t.\tID=gene6;Dbxref=GeneID:106578259;Name=LOC106578259;end_range=362950,.;gbkey=Gene;gene=LOC106578259;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tgene\t399123\t401622\t.\t+\t.\tID=gene7;Dbxref=GeneID:106583877;Name=LOC106583877;gbkey=Gene;gene=LOC106583877;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tgene\t432556\t435055\t.\t-\t.\tID=gene8;Dbxref=GeneID:106589664;Name=LOC106589664;gbkey=Gene;gene=LOC106589664;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tgene\t446612\t449111\t.\t+\t.\tID=gene9;Dbxref=GeneID:106596642;Name=LOC106596642;end_range=490663,.;gbkey=Gene;gene=LOC106596642;gene_biotype=protein_coding;partial=true\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/flankBed \\\n",
    "-i ref_ICSASG_v2_top_level.gene.noNW.gff3 \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-l 2500 \\\n",
    "-r 0 -s |\\\n",
    "head"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#print \"put_promoter\" instead of gene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tput_promoter\t62140\t64639\t.\t-\t.\tID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t198816\t201315\t.\t-\t.\tID=gene1;Dbxref=GeneID:106607996;Name=LOC106607996;gbkey=Gene;gene=LOC106607996;gene_biotype=protein_coding;partial=true;start_range=.,160437\n",
      "NC_027300.1\tGnomon\tput_promoter\t231472\t233971\t.\t-\t.\tID=gene2;Dbxref=GeneID:106601976;Name=LOC106601976;end_range=231471,.;gbkey=Gene;gene=LOC106601976;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tput_promoter\t297112\t299611\t.\t-\t.\tID=gene3;Dbxref=GeneID:106560213;Name=LOC106560213;gbkey=Gene;gene=LOC106560213;gene_biotype=protein_coding;partial=true;start_range=.,296031\n",
      "NC_027300.1\tGnomon\tput_promoter\t304442\t306941\t.\t+\t.\tID=gene4;Dbxref=GeneID:106566220;Name=LOC106566220;gbkey=Gene;gene=LOC106566220;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t346455\t348954\t.\t-\t.\tID=gene5;Dbxref=GeneID:106571988;Name=LOC106571988;end_range=346454,.;gbkey=Gene;gene=LOC106571988;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tput_promoter\t353175\t355674\t.\t+\t.\tID=gene6;Dbxref=GeneID:106578259;Name=LOC106578259;end_range=362950,.;gbkey=Gene;gene=LOC106578259;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tput_promoter\t399123\t401622\t.\t+\t.\tID=gene7;Dbxref=GeneID:106583877;Name=LOC106583877;gbkey=Gene;gene=LOC106583877;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t432556\t435055\t.\t-\t.\tID=gene8;Dbxref=GeneID:106589664;Name=LOC106589664;gbkey=Gene;gene=LOC106589664;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t446612\t449111\t.\t+\t.\tID=gene9;Dbxref=GeneID:106596642;Name=LOC106596642;end_range=490663,.;gbkey=Gene;gene=LOC106596642;gene_biotype=protein_coding;partial=true\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/flankBed \\\n",
    "-i ref_ICSASG_v2_top_level.gene.noNW.gff3 \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-l 2500 \\\n",
    "-r 0 -s |\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{gsub(\"gene\",\"put_promoter\",$3); print $0 }'|\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{if($5-$4 > 3)print $0}'|\\\n",
    "head"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/flankBed \\\n",
    "-i ref_ICSASG_v2_top_level.gene.noNW.gff3 \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-l 2500 \\\n",
    "-r 0 -s |\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{gsub(\"gene\",\"put_promoter\",$3); print $0 }'|\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{if($5-$4 > 3)print $0}'\\\n",
    "> ref_ICSASG_v2_top_level.GenePromoter.gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tput_promoter\t62140\t64639\t.\t-\t.\tID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t198816\t201315\t.\t-\t.\tID=gene1;Dbxref=GeneID:106607996;Name=LOC106607996;gbkey=Gene;gene=LOC106607996;gene_biotype=protein_coding;partial=true;start_range=.,160437\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t231472\t233971\t.\t-\t.\tID=gene2;Dbxref=GeneID:106601976;Name=LOC106601976;end_range=231471,.;gbkey=Gene;gene=LOC106601976;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t297112\t299611\t.\t-\t.\tID=gene3;Dbxref=GeneID:106560213;Name=LOC106560213;gbkey=Gene;gene=LOC106560213;gene_biotype=protein_coding;partial=true;start_range=.,296031\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t304442\t306941\t.\t+\t.\tID=gene4;Dbxref=GeneID:106566220;Name=LOC106566220;gbkey=Gene;gene=LOC106566220;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t346455\t348954\t.\t-\t.\tID=gene5;Dbxref=GeneID:106571988;Name=LOC106571988;end_range=346454,.;gbkey=Gene;gene=LOC106571988;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t353175\t355674\t.\t+\t.\tID=gene6;Dbxref=GeneID:106578259;Name=LOC106578259;end_range=362950,.;gbkey=Gene;gene=LOC106578259;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t399123\t401622\t.\t+\t.\tID=gene7;Dbxref=GeneID:106583877;Name=LOC106583877;gbkey=Gene;gene=LOC106583877;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t432556\t435055\t.\t-\t.\tID=gene8;Dbxref=GeneID:106589664;Name=LOC106589664;gbkey=Gene;gene=LOC106589664;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t446612\t449111\t.\t+\t.\tID=gene9;Dbxref=GeneID:106596642;Name=LOC106596642;end_range=490663,.;gbkey=Gene;gene=LOC106596642;gene_biotype=protein_coding;partial=true\r\n"
     ]
    }
   ],
   "source": [
    "!head ref_ICSASG_v2_top_level.GenePromoter.gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   52273 ref_ICSASG_v2_top_level.GenePromoter.gff\r\n"
     ]
    }
   ],
   "source": [
    "!wc -l ref_ICSASG_v2_top_level.GenePromoter.gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#create bed file of 3' UTR track "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tput_promoter\t3001\t5500\t.\t-\t.\tID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t157937\t160436\t.\t-\t.\tID=gene1;Dbxref=GeneID:106607996;Name=LOC106607996;gbkey=Gene;gene=LOC106607996;gene_biotype=protein_coding;partial=true;start_range=.,160437\n",
      "NC_027300.1\tGnomon\tput_promoter\t225830\t228329\t.\t-\t.\tID=gene2;Dbxref=GeneID:106601976;Name=LOC106601976;end_range=231471,.;gbkey=Gene;gene=LOC106601976;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tput_promoter\t293531\t296030\t.\t-\t.\tID=gene3;Dbxref=GeneID:106560213;Name=LOC106560213;gbkey=Gene;gene=LOC106560213;gene_biotype=protein_coding;partial=true;start_range=.,296031\n",
      "NC_027300.1\tGnomon\tput_promoter\t310879\t313378\t.\t+\t.\tID=gene4;Dbxref=GeneID:106566220;Name=LOC106566220;gbkey=Gene;gene=LOC106566220;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t328869\t331368\t.\t-\t.\tID=gene5;Dbxref=GeneID:106571988;Name=LOC106571988;end_range=346454,.;gbkey=Gene;gene=LOC106571988;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tput_promoter\t362951\t365450\t.\t+\t.\tID=gene6;Dbxref=GeneID:106578259;Name=LOC106578259;end_range=362950,.;gbkey=Gene;gene=LOC106578259;gene_biotype=protein_coding;partial=true\n",
      "NC_027300.1\tGnomon\tput_promoter\t416795\t419294\t.\t+\t.\tID=gene7;Dbxref=GeneID:106583877;Name=LOC106583877;gbkey=Gene;gene=LOC106583877;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t429162\t431661\t.\t-\t.\tID=gene8;Dbxref=GeneID:106589664;Name=LOC106589664;gbkey=Gene;gene=LOC106589664;gene_biotype=protein_coding\n",
      "NC_027300.1\tGnomon\tput_promoter\t490664\t493163\t.\t+\t.\tID=gene9;Dbxref=GeneID:106596642;Name=LOC106596642;end_range=490663,.;gbkey=Gene;gene=LOC106596642;gene_biotype=protein_coding;partial=true\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/flankBed \\\n",
    "-i ref_ICSASG_v2_top_level.gene.noNW.gff3 \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-l 0 \\\n",
    "-r 2500 -s|\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{gsub(\"gene\",\"put_promoter\",$3); print $0 }'|\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{if($5-$4 > 3)print $0}'|\\\n",
    "head"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/flankBed \\\n",
    "-i ref_ICSASG_v2_top_level.gene.noNW.gff3 \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-l 0 \\\n",
    "-r 2500 -s|\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{gsub(\"gene\",\"put_promoter\",$3); print $0 }'|\\\n",
    "awk -F\"\\t\" '{OFS=FS=\"\\t\"}{if($5-$4 > 3)print $0}'\\\n",
    "> ref_ICSASG_v2_top_level.Gene3primerUTR.gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tput_promoter\t3001\t5500\t.\t-\t.\tID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t157937\t160436\t.\t-\t.\tID=gene1;Dbxref=GeneID:106607996;Name=LOC106607996;gbkey=Gene;gene=LOC106607996;gene_biotype=protein_coding;partial=true;start_range=.,160437\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t225830\t228329\t.\t-\t.\tID=gene2;Dbxref=GeneID:106601976;Name=LOC106601976;end_range=231471,.;gbkey=Gene;gene=LOC106601976;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t293531\t296030\t.\t-\t.\tID=gene3;Dbxref=GeneID:106560213;Name=LOC106560213;gbkey=Gene;gene=LOC106560213;gene_biotype=protein_coding;partial=true;start_range=.,296031\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t310879\t313378\t.\t+\t.\tID=gene4;Dbxref=GeneID:106566220;Name=LOC106566220;gbkey=Gene;gene=LOC106566220;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t328869\t331368\t.\t-\t.\tID=gene5;Dbxref=GeneID:106571988;Name=LOC106571988;end_range=346454,.;gbkey=Gene;gene=LOC106571988;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t362951\t365450\t.\t+\t.\tID=gene6;Dbxref=GeneID:106578259;Name=LOC106578259;end_range=362950,.;gbkey=Gene;gene=LOC106578259;gene_biotype=protein_coding;partial=true\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t416795\t419294\t.\t+\t.\tID=gene7;Dbxref=GeneID:106583877;Name=LOC106583877;gbkey=Gene;gene=LOC106583877;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t429162\t431661\t.\t-\t.\tID=gene8;Dbxref=GeneID:106589664;Name=LOC106589664;gbkey=Gene;gene=LOC106589664;gene_biotype=protein_coding\r\n",
      "NC_027300.1\tGnomon\tput_promoter\t490664\t493163\t.\t+\t.\tID=gene9;Dbxref=GeneID:106596642;Name=LOC106596642;end_range=490663,.;gbkey=Gene;gene=LOC106596642;gene_biotype=protein_coding;partial=true\r\n"
     ]
    }
   ],
   "source": [
    "!head ref_ICSASG_v2_top_level.Gene3primerUTR.gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#create bed file of genome binned into 250 bp windows"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\t0\t250\n",
      "NC_027300.1\t250\t500\n",
      "NC_027300.1\t500\t750\n",
      "NC_027300.1\t750\t1000\n",
      "NC_027300.1\t1000\t1250\n",
      "NC_027300.1\t1250\t1500\n",
      "NC_027300.1\t1500\t1750\n",
      "NC_027300.1\t1750\t2000\n",
      "NC_027300.1\t2000\t2250\n",
      "NC_027300.1\t2250\t2500\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/windowMaker \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-w 250 |\\\n",
    "head\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#looks good so save output to file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/windowMaker \\\n",
    "-g GCF_000233375.1_ICSASG_v2_genomic.fa.fai \\\n",
    "-w 250 \\\n",
    "> GCF_000233375.1_ICSASG_v2_genomic.250bp.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DEG_salinity.bed\r\n",
      "DEG_salinity_NCid.bed\r\n",
      "DEG_salinity_NCid_sorted.bed\r\n",
      "DEG_salinity_gff.txt\r\n",
      "DEG_salinity_protein_info.txt\r\n",
      "DEG_temperature.bed\r\n",
      "DEG_temperature_NCid.bed\r\n",
      "DMR1_test.fa\r\n",
      "DMR_2way_aov_tuk_modelsumm_0.05.bed\r\n",
      "GCF_000233375.1_ICSASG_v2_genomic.250bp.bed\r\n",
      "GCF_000233375.1_ICSASG_v2_genomic.fa.fai\r\n",
      "HoxC9_humanTargets.txt\r\n",
      "List of DE genes.xlsx\r\n",
      "TempXSal_DMR_tuk0.05_anno.txt\r\n",
      "allc_5x_0.75Xgrp_CpG.txt\r\n",
      "allc_5x_CpG.txt\r\n",
      "chr_5x0.75grp_cov.txt\r\n",
      "chr_name_conversion.txt\r\n",
      "mrna_flank2.5k.gff\r\n",
      "ref_ICSASG_v2_top_level.Gene3primerUTR.bed\r\n",
      "ref_ICSASG_v2_top_level.GenePromoter.bed\r\n",
      "ref_ICSASG_v2_top_level.gene.gff3\r\n",
      "\u001b[31mref_ICSASG_v2_top_level.gff3\u001b[m\u001b[m\r\n"
     ]
    }
   ],
   "source": [
    "!ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#copy new bed files to gannet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ref_ICSASG_v2_top_level.GenePromoter.gff\n",
      "     8932677 100%   19.65MB/s    0:00:00 (xfer#1, to-check=0/1)\n",
      "\n",
      "sent 8933886 bytes  received 42 bytes  5955952.00 bytes/sec\n",
      "total size is 8932677  speedup is 1.00\n"
     ]
    }
   ],
   "source": [
    "!rsync --progress --verbose ref_ICSASG_v2_top_level.GenePromoter.gff \\\n",
    "/Volumes/web/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq/chr1-29MT"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GCF_000233375.1_ICSASG_v2_genomic.250bp.bed\n",
      "   267277748 100%   44.06MB/s    0:00:05 (xfer#1, to-check=0/1)\n",
      "\n",
      "sent 267310496 bytes  received 42 bytes  41124698.15 bytes/sec\n",
      "total size is 267277748  speedup is 1.00\n"
     ]
    }
   ],
   "source": [
    "!rsync --progress --verbose GCF_000233375.1_ICSASG_v2_genomic.250bp.bed \\\n",
    "/Volumes/web/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq/chr1-29MT"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ref_ICSASG_v2_top_level.Gene3primerUTR.gff\n",
      "     8932689 100%   21.60MB/s    0:00:00 (xfer#1, to-check=0/1)\n",
      "\n",
      "sent 8933900 bytes  received 42 bytes  5955961.33 bytes/sec\n",
      "total size is 8932689  speedup is 1.00\n"
     ]
    }
   ],
   "source": [
    "!rsync --progress --verbose ref_ICSASG_v2_top_level.Gene3primerUTR.gff \\\n",
    "/Volumes/web/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq/chr1-29MT"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Check if mRNA track is the same as CDS track"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "cat ref_ICSASG_v2_top_level.gff3 |\\\n",
    "awk '{if($3 == \"CDS\")print $0}'|\\\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/sortBed \\\n",
    "> ref_ICSASG_v2_top_level.CDS.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "cat ref_ICSASG_v2_top_level.gff3 |\\\n",
    "awk '{if($3 == \"mRNA\")print $0}'|\\\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/sortBed \\\n",
    "> ref_ICSASG_v2_top_level.mRNA.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "cat ref_ICSASG_v2_top_level.gff3 |\\\n",
    "awk '{if($3 == \"exon\")print $0}' |\\\n",
    "/Users/Shared/bioinformatics/bedtools2/bin/sortBed \\\n",
    "> ref_ICSASG_v2_top_level.exon.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_027300.1\tGnomon\tmRNA\t5692\t16965\t.\t-\t.\tID=rna0;Parent=gene0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;Name=XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t17020\t23977\t.\t-\t.\tID=rna0;Parent=gene0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;Name=XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t24242\t43485\t.\t-\t.\tID=rna0;Parent=gene0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;Name=XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t43634\t62139\t.\t-\t.\tID=rna0;Parent=gene0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;Name=XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t160639\t160912\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t161020\t161136\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t161279\t162534\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t162652\t164904\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t165175\t165281\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t165386\t171855\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t172059\t173080\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t173238\t174828\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t175009\t182296\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t182486\t182575\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t182703\t185825\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t186144\t190582\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t190699\t190820\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t190878\t190972\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t191136\t195216\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t195652\t195790\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t195961\t196139\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t196306\t196549\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t197189\t198815\t.\t-\t.\tID=rna1;Parent=gene1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Name=XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;start_range=.,160437;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t228330\t228934\t.\t-\t.\tID=rna2;Parent=gene2;Dbxref=GeneID:106601976,Genbank:XM_014198158.1;Name=XM_014198158.1;end_range=231471,.;gbkey=mRNA;gene=LOC106601976;partial=true;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014198158.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t229142\t230208\t.\t-\t.\tID=rna2;Parent=gene2;Dbxref=GeneID:106601976,Genbank:XM_014198158.1;Name=XM_014198158.1;end_range=231471,.;gbkey=mRNA;gene=LOC106601976;partial=true;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014198158.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t230315\t231333\t.\t-\t.\tID=rna2;Parent=gene2;Dbxref=GeneID:106601976,Genbank:XM_014198158.1;Name=XM_014198158.1;end_range=231471,.;gbkey=mRNA;gene=LOC106601976;partial=true;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014198158.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t296099\t296290\t.\t-\t.\tID=rna3;Parent=gene3;Dbxref=GeneID:106560213,Genbank:XM_014126719.1;Name=XM_014126719.1;gbkey=mRNA;gene=LOC106560213;partial=true;product=phospholipase B1%2C membrane-associated-like;start_range=.,296031;transcript_id=XM_014126719.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t296350\t296596\t.\t-\t.\tID=rna3;Parent=gene3;Dbxref=GeneID:106560213,Genbank:XM_014126719.1;Name=XM_014126719.1;gbkey=mRNA;gene=LOC106560213;partial=true;product=phospholipase B1%2C membrane-associated-like;start_range=.,296031;transcript_id=XM_014126719.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t296673\t296758\t.\t-\t.\tID=rna3;Parent=gene3;Dbxref=GeneID:106560213,Genbank:XM_014126719.1;Name=XM_014126719.1;gbkey=mRNA;gene=LOC106560213;partial=true;product=phospholipase B1%2C membrane-associated-like;start_range=.,296031;transcript_id=XM_014126719.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t296818\t296983\t.\t-\t.\tID=rna3;Parent=gene3;Dbxref=GeneID:106560213,Genbank:XM_014126719.1;Name=XM_014126719.1;gbkey=mRNA;gene=LOC106560213;partial=true;product=phospholipase B1%2C membrane-associated-like;start_range=.,296031;transcript_id=XM_014126719.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t297033\t297111\t.\t-\t.\tID=rna3;Parent=gene3;Dbxref=GeneID:106560213,Genbank:XM_014126719.1;Name=XM_014126719.1;gbkey=mRNA;gene=LOC106560213;partial=true;product=phospholipase B1%2C membrane-associated-like;start_range=.,296031;transcript_id=XM_014126719.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t306942\t307021\t.\t+\t.\tID=rna4;Parent=gene4;Dbxref=GeneID:106566220,Genbank:XM_014138059.1;Name=XM_014138059.1;gbkey=mRNA;gene=LOC106566220;product=forkhead box protein I1c-like;transcript_id=XM_014138059.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t307605\t309990\t.\t+\t.\tID=rna4;Parent=gene4;Dbxref=GeneID:106566220,Genbank:XM_014138059.1;Name=XM_014138059.1;gbkey=mRNA;gene=LOC106566220;product=forkhead box protein I1c-like;transcript_id=XM_014138059.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t310635\t310878\t.\t+\t.\tID=rna4;Parent=gene4;Dbxref=GeneID:106566220,Genbank:XM_014138059.1;Name=XM_014138059.1;gbkey=mRNA;gene=LOC106566220;product=forkhead box protein I1c-like;transcript_id=XM_014138059.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t331369\t331483\t.\t-\t.\tID=rna5;Parent=gene5;Dbxref=GeneID:106571988,Genbank:XM_014149530.1;Name=XM_014149530.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 721 bases not found in genome assembly;end_range=346454,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106571988;partial=true;product=GDNF family receptor alpha-4-like;transcript_id=XM_014149530.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t331631\t334436\t.\t-\t.\tID=rna5;Parent=gene5;Dbxref=GeneID:106571988,Genbank:XM_014149530.1;Name=XM_014149530.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 721 bases not found in genome assembly;end_range=346454,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106571988;partial=true;product=GDNF family receptor alpha-4-like;transcript_id=XM_014149530.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t334598\t346319\t.\t-\t.\tID=rna5;Parent=gene5;Dbxref=GeneID:106571988,Genbank:XM_014149530.1;Name=XM_014149530.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 721 bases not found in genome assembly;end_range=346454,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106571988;partial=true;product=GDNF family receptor alpha-4-like;transcript_id=XM_014149530.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t355839\t356962\t.\t+\t.\tID=rna6;Parent=gene6;Dbxref=GeneID:106578259,Genbank:XM_014160785.1;Name=XM_014160785.1;end_range=362950,.;gbkey=mRNA;gene=LOC106578259;partial=true;product=attractin-like;transcript_id=XM_014160785.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t357092\t360282\t.\t+\t.\tID=rna6;Parent=gene6;Dbxref=GeneID:106578259,Genbank:XM_014160785.1;Name=XM_014160785.1;end_range=362950,.;gbkey=mRNA;gene=LOC106578259;partial=true;product=attractin-like;transcript_id=XM_014160785.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t360486\t362781\t.\t+\t.\tID=rna6;Parent=gene6;Dbxref=GeneID:106578259,Genbank:XM_014160785.1;Name=XM_014160785.1;end_range=362950,.;gbkey=mRNA;gene=LOC106578259;partial=true;product=attractin-like;transcript_id=XM_014160785.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t401623\t401918\t.\t+\t.\tID=rna7;Parent=gene7;Dbxref=GeneID:106583877,Genbank:XM_014172412.1;Name=XM_014172412.1;gbkey=mRNA;gene=LOC106583877;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014172412.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t402136\t408323\t.\t+\t.\tID=rna7;Parent=gene7;Dbxref=GeneID:106583877,Genbank:XM_014172412.1;Name=XM_014172412.1;gbkey=mRNA;gene=LOC106583877;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014172412.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t408406\t413410\t.\t+\t.\tID=rna7;Parent=gene7;Dbxref=GeneID:106583877,Genbank:XM_014172412.1;Name=XM_014172412.1;gbkey=mRNA;gene=LOC106583877;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014172412.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t413535\t416515\t.\t+\t.\tID=rna7;Parent=gene7;Dbxref=GeneID:106583877,Genbank:XM_014172412.1;Name=XM_014172412.1;gbkey=mRNA;gene=LOC106583877;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014172412.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t449124\t458417\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t458503\t459179\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t459306\t459423\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t459538\t461686\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t461820\t463442\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t463517\t472763\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t473017\t476180\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t476288\t477668\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t477835\t477958\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t478133\t490467\t.\t+\t.\tID=rna9;Parent=gene9;Dbxref=GeneID:106596642,Genbank:XM_014189536.1;Name=XM_014189536.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 54 bases not found in genome assembly;end_range=490663,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106596642;partial=true;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014189536.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t516060\t516192\t.\t+\t.\tID=rna10;Parent=gene10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;Name=XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t516436\t518605\t.\t+\t.\tID=rna10;Parent=gene10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;Name=XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t518667\t518790\t.\t+\t.\tID=rna10;Parent=gene10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;Name=XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t518847\t518943\t.\t+\t.\tID=rna10;Parent=gene10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;Name=XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t519004\t519177\t.\t+\t.\tID=rna10;Parent=gene10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;Name=XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t519247\t519262\t.\t+\t.\tID=rna10;Parent=gene10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;Name=XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t521119\t521277\t.\t+\t.\tID=rna11;Parent=gene11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Name=XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;end_range=525615,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t521521\t523667\t.\t+\t.\tID=rna11;Parent=gene11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Name=XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;end_range=525615,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t523729\t523852\t.\t+\t.\tID=rna11;Parent=gene11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Name=XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;end_range=525615,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t523909\t524005\t.\t+\t.\tID=rna11;Parent=gene11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Name=XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;end_range=525615,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t524066\t524239\t.\t+\t.\tID=rna11;Parent=gene11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Name=XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;end_range=525615,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t524305\t525546\t.\t+\t.\tID=rna11;Parent=gene11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Name=XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;end_range=525615,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t546224\t546648\t.\t+\t.\tID=rna12;Parent=gene12;Dbxref=GeneID:106601271,Genbank:XM_014193723.1;Name=XM_014193723.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X1;transcript_id=XM_014193723.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t547127\t547789\t.\t+\t.\tID=rna12;Parent=gene12;Dbxref=GeneID:106601271,Genbank:XM_014193723.1;Name=XM_014193723.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X1;transcript_id=XM_014193723.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t547888\t549216\t.\t+\t.\tID=rna12;Parent=gene12;Dbxref=GeneID:106601271,Genbank:XM_014193723.1;Name=XM_014193723.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X1;transcript_id=XM_014193723.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t546226\t546648\t.\t+\t.\tID=rna13;Parent=gene12;Dbxref=GeneID:106601271,Genbank:XM_014194419.1;Name=XM_014194419.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X2;transcript_id=XM_014194419.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t547127\t547789\t.\t+\t.\tID=rna13;Parent=gene12;Dbxref=GeneID:106601271,Genbank:XM_014194419.1;Name=XM_014194419.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X2;transcript_id=XM_014194419.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t547888\t549216\t.\t+\t.\tID=rna13;Parent=gene12;Dbxref=GeneID:106601271,Genbank:XM_014194419.1;Name=XM_014194419.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X2;transcript_id=XM_014194419.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t565022\t565329\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t565403\t566839\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t566921\t574698\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t574764\t585359\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t585518\t588128\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t588314\t588518\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t588731\t601306\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t601475\t601676\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t601794\t602699\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t603234\t604877\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t605025\t608421\t.\t+\t.\tID=rna14;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;Name=XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t565022\t565329\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t565403\t566839\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t566921\t574698\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t574764\t585359\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t585518\t588128\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t588314\t588518\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t588731\t601306\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t601475\t601676\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t601794\t602699\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t603234\t604877\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t605025\t605196\t.\t+\t.\tID=rna15;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;Name=XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t565022\t565329\t.\t+\t.\tID=rna16;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;Name=XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t565403\t566839\t.\t+\t.\tID=rna16;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;Name=XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t566921\t574698\t.\t+\t.\tID=rna16;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;Name=XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t574764\t585359\t.\t+\t.\tID=rna16;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;Name=XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t585518\t588128\t.\t+\t.\tID=rna16;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;Name=XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\tmRNA\t588314\t588518\t.\t+\t.\tID=rna16;Parent=gene13;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;Name=XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n"
     ]
    }
   ],
   "source": [
    "!/Users/Shared/bioinformatics/bedtools2/bin/subtractBed \\\n",
    "-a ref_ICSASG_v2_top_level.mRNA.gff3 \\\n",
    "-b ref_ICSASG_v2_top_level.CDS.gff3 |\\\n",
    "head -100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_001960.1\tRefSeq\texon\t1007\t1074\t.\t+\t.\tID=id1546210;Parent=rna133438;anticodon=(pos:1037..1039);gbkey=tRNA;product=tRNA-Phe\r\n",
      "NC_001960.1\tRefSeq\texon\t1075\t2020\t.\t+\t.\tID=id1546211;Parent=rna133439;gbkey=rRNA;product=12S ribosomal RNA\r\n",
      "NC_001960.1\tRefSeq\texon\t2021\t2092\t.\t+\t.\tID=id1546212;Parent=rna133440;anticodon=(pos:2054..2056);gbkey=tRNA;product=tRNA-Val\r\n",
      "NC_001960.1\tRefSeq\texon\t2093\t3770\t.\t+\t.\tID=id1546213;Parent=rna133441;gbkey=rRNA;product=16S ribosomal RNA\r\n",
      "NC_001960.1\tRefSeq\texon\t3771\t3845\t.\t+\t.\tID=id1546214;Parent=rna133442;anticodon=(pos:3806..3808);codons=2%2C3;gbkey=tRNA;product=tRNA-Leu\r\n",
      "NC_001960.1\tRefSeq\texon\t4828\t4899\t.\t+\t.\tID=id1546215;Parent=rna133443;anticodon=(pos:4860..4862);gbkey=tRNA;product=tRNA-Ile\r\n",
      "NC_001960.1\tRefSeq\texon\t4897\t4967\t.\t-\t.\tID=id1546216;Parent=rna133444;anticodon=(pos:complement(4933..4935));gbkey=tRNA;product=tRNA-Gln\r\n",
      "NC_001960.1\tRefSeq\texon\t4967\t5035\t.\t+\t.\tID=id1546217;Parent=rna133445;anticodon=(pos:4997..4999);gbkey=tRNA;product=tRNA-Met\r\n",
      "NC_001960.1\tRefSeq\texon\t6088\t6156\t.\t+\t.\tID=id1546218;Parent=rna133446;anticodon=(pos:6120..6122);gbkey=tRNA;product=tRNA-Trp\r\n",
      "NC_001960.1\tRefSeq\texon\t6160\t6228\t.\t-\t.\tID=id1546219;Parent=rna133447;anticodon=(pos:complement(6196..6198));gbkey=tRNA;product=tRNA-Ala\r\n",
      "NC_001960.1\tRefSeq\texon\t6230\t6302\t.\t-\t.\tID=id1546220;Parent=rna133448;anticodon=(pos:complement(6267..6269));gbkey=tRNA;product=tRNA-Asn\r\n",
      "NC_001960.1\tRefSeq\texon\t6337\t6403\t.\t-\t.\tID=id1546222;Parent=rna133449;anticodon=(pos:complement(6373..6375));gbkey=tRNA;product=tRNA-Cys\r\n",
      "NC_001960.1\tRefSeq\texon\t6404\t6474\t.\t-\t.\tID=id1546223;Parent=rna133450;anticodon=(pos:complement(6440..6442));gbkey=tRNA;product=tRNA-Tyr\r\n",
      "NC_001960.1\tRefSeq\texon\t8027\t8097\t.\t-\t.\tID=id1546224;Parent=rna133451;anticodon=(pos:complement(8063..8065));codons=4%2C5%2C6%2C7;gbkey=tRNA;product=tRNA-Ser\r\n",
      "NC_001960.1\tRefSeq\texon\t8102\t8175\t.\t+\t.\tID=id1546225;Parent=rna133452;anticodon=(pos:8137..8139);gbkey=tRNA;product=tRNA-Asp\r\n",
      "NC_001960.1\tRefSeq\texon\t8881\t8954\t.\t+\t.\tID=id1546226;Parent=rna133453;anticodon=(pos:8915..8917);gbkey=tRNA;product=tRNA-Lys\r\n",
      "NC_001960.1\tRefSeq\texon\t10583\t10651\t.\t+\t.\tID=id1546227;Parent=rna133454;anticodon=(pos:10613..10615);gbkey=tRNA;gene=COX3;product=tRNA-Gly\r\n",
      "NC_001960.1\tRefSeq\texon\t11001\t11070\t.\t+\t.\tID=id1546228;Parent=rna133455;anticodon=(pos:11032..11034);gbkey=tRNA;product=tRNA-Arg\r\n",
      "NC_001960.1\tRefSeq\texon\t12742\t12810\t.\t+\t.\tID=id1546229;Parent=rna133456;anticodon=(pos:12772..12774);gbkey=tRNA;product=tRNA-His\r\n",
      "NC_001960.1\tRefSeq\texon\t12811\t12879\t.\t+\t.\tID=id1546230;Parent=rna133457;anticodon=(pos:12838..12840);codons=44%2C45;gbkey=tRNA;product=tRNA-Ser\r\n",
      "NC_001960.1\tRefSeq\texon\t12881\t12953\t.\t+\t.\tID=id1546231;Parent=rna133458;anticodon=(pos:12914..12916);codons=16%2C17%2C18%2C19;gbkey=tRNA;product=tRNA-Leu\r\n",
      "NC_001960.1\tRefSeq\texon\t15311\t15379\t.\t-\t.\tID=id1546232;Parent=rna133459;anticodon=(pos:complement(15347..15349));gbkey=tRNA;product=tRNA-Glu\r\n",
      "NC_001960.1\tRefSeq\texon\t16525\t16596\t.\t+\t.\tID=id1546233;Parent=rna133460;anticodon=(pos:16557..16559);gbkey=tRNA;product=tRNA-Thr\r\n",
      "NC_001960.1\tRefSeq\texon\t16596\t16665\t.\t-\t.\tID=id1546234;Parent=rna133461;anticodon=(pos:complement(16632..16634));gbkey=tRNA;product=tRNA-Pro\r\n",
      "NC_027300.1\tGnomon\texon\t43634\t43714\t.\t-\t.\tID=id2;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1\r\n",
      "NC_027300.1\tGnomon\texon\t61647\t62139\t.\t-\t.\tID=id1;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1\r\n",
      "NC_027300.1\tGnomon\texon\t197189\t197213\t.\t-\t.\tID=id7;Parent=rna1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\texon\t198682\t198815\t.\t-\t.\tID=id6;Parent=rna1;Dbxref=GeneID:106607996,Genbank:XM_014209195.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 1366 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106607996;partial=true;product=histone-lysine N-methyltransferase NSD2-like;transcript_id=XM_014209195.1\r\n",
      "NC_027300.1\tGnomon\texon\t228330\t228934\t.\t-\t.\tID=id28;Parent=rna2;Dbxref=GeneID:106601976,Genbank:XM_014198158.1;gbkey=mRNA;gene=LOC106601976;partial=true;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014198158.1\r\n",
      "NC_027300.1\tGnomon\texon\t297033\t297111\t.\t-\t.\tID=id29;Parent=rna3;Dbxref=GeneID:106560213,Genbank:XM_014126719.1;gbkey=mRNA;gene=LOC106560213;partial=true;product=phospholipase B1%2C membrane-associated-like;transcript_id=XM_014126719.1\r\n",
      "NC_027300.1\tGnomon\texon\t306942\t307021\t.\t+\t.\tID=id34;Parent=rna4;Dbxref=GeneID:106566220,Genbank:XM_014138059.1;gbkey=mRNA;gene=LOC106566220;product=forkhead box protein I1c-like;transcript_id=XM_014138059.1\r\n",
      "NC_027300.1\tGnomon\texon\t310635\t310878\t.\t+\t.\tID=id35;Parent=rna4;Dbxref=GeneID:106566220,Genbank:XM_014138059.1;gbkey=mRNA;gene=LOC106566220;product=forkhead box protein I1c-like;transcript_id=XM_014138059.1\r\n",
      "NC_027300.1\tGnomon\texon\t331369\t331483\t.\t-\t.\tID=id38;Parent=rna5;Dbxref=GeneID:106571988,Genbank:XM_014149530.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 721 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106571988;partial=true;product=GDNF family receptor alpha-4-like;transcript_id=XM_014149530.1\r\n",
      "NC_027300.1\tGnomon\texon\t401623\t401679\t.\t+\t.\tID=id43;Parent=rna7;Dbxref=GeneID:106583877,Genbank:XM_014172412.1;gbkey=mRNA;gene=LOC106583877;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014172412.1\r\n",
      "NC_027300.1\tGnomon\texon\t401907\t401918\t.\t+\t.\tID=id44;Parent=rna7;Dbxref=GeneID:106583877,Genbank:XM_014172412.1;gbkey=mRNA;gene=LOC106583877;product=sodium bicarbonate transporter-like protein 11;transcript_id=XM_014172412.1\r\n",
      "NC_027300.1\tGnomon\texon\t516060\t516192\t.\t+\t.\tID=id60;Parent=rna10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\texon\t519247\t519262\t.\t+\t.\tID=id64;Parent=rna10;Dbxref=GeneID:106599499,Genbank:XM_014191287.1;gbkey=mRNA;gene=LOC106599499;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014191287.1\r\n",
      "NC_027300.1\tGnomon\texon\t521119\t521277\t.\t+\t.\tID=id65;Parent=rna11;Dbxref=GeneID:106600683,Genbank:XM_014192572.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 519 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=LOC106600683;partial=true;product=ribose-5-phosphate isomerase-like;transcript_id=XM_014192572.1\r\n",
      "NC_027300.1\tGnomon\texon\t546224\t546648\t.\t+\t.\tID=id71;Parent=rna12;Dbxref=GeneID:106601271,Genbank:XM_014193723.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X1;transcript_id=XM_014193723.1\r\n",
      "NC_027300.1\tGnomon\texon\t546226\t546648\t.\t+\t.\tID=id73;Parent=rna13;Dbxref=GeneID:106601271,Genbank:XM_014194419.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X2;transcript_id=XM_014194419.1\r\n",
      "NC_027300.1\tGnomon\texon\t547888\t549216\t.\t+\t.\tID=id72;Parent=rna12;Dbxref=GeneID:106601271,Genbank:XM_014193723.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X1;transcript_id=XM_014193723.1\r\n",
      "NC_027300.1\tGnomon\texon\t547888\t549216\t.\t+\t.\tID=id75;Parent=rna13;Dbxref=GeneID:106601271,Genbank:XM_014194419.1;gbkey=mRNA;gene=LOC106601271;product=uncharacterized LOC106601271%2C transcript variant X2;transcript_id=XM_014194419.1\r\n",
      "NC_027300.1\tGnomon\texon\t565022\t565329\t.\t+\t.\tID=id76;Parent=rna14;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\texon\t565022\t565329\t.\t+\t.\tID=id98;Parent=rna16;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\texon\t565022\t565329\t.\t+\t.\tID=id87;Parent=rna15;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\ttRNAscan-SE\texon\t572338\t572410\t.\t-\t.\tID=id109;Parent=rna17;Dbxref=GeneID:106455102;Note=transfer RNA alanine (anticodon UGC);anticodon=(pos:complement(572375..572377));gbkey=tRNA;gene=trnaa-ugc;product=tRNA-Ala\r\n",
      "NC_027300.1\tGnomon\texon\t605025\t605058\t.\t+\t.\tID=id85;Parent=rna14;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\texon\t605025\t605040\t.\t+\t.\tID=id96;Parent=rna15;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\texon\t605025\t605058\t.\t+\t.\tID=id107;Parent=rna16;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\texon\t605119\t605196\t.\t+\t.\tID=id97;Parent=rna15;Dbxref=GeneID:106602449,Genbank:XM_014196129.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X2;transcript_id=XM_014196129.1\r\n",
      "NC_027300.1\tGnomon\texon\t605137\t605188\t.\t+\t.\tID=id108;Parent=rna16;Dbxref=GeneID:106602449,Genbank:XM_014196954.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X3;transcript_id=XM_014196954.1\r\n",
      "NC_027300.1\tGnomon\texon\t608277\t608421\t.\t+\t.\tID=id86;Parent=rna14;Dbxref=GeneID:106602449,Genbank:XM_014195458.1;gbkey=mRNA;gene=jade1;product=jade family PHD finger 1%2C transcript variant X1;transcript_id=XM_014195458.1\r\n",
      "NC_027300.1\tGnomon\texon\t654311\t654319\t.\t+\t.\tID=id110;Parent=rna18;Dbxref=GeneID:106604115,Genbank:XM_014198842.1;gbkey=mRNA;gene=LOC106604115;product=attractin-like;transcript_id=XM_014198842.1\r\n",
      "NC_027300.1\tGnomon\texon\t657676\t657775\t.\t+\t.\tID=id112;Parent=rna18;Dbxref=GeneID:106604115,Genbank:XM_014198842.1;gbkey=mRNA;gene=LOC106604115;product=attractin-like;transcript_id=XM_014198842.1\r\n",
      "NC_027300.1\tGnomon\texon\t888307\t888313\t.\t+\t.\tID=id115;Parent=rna20;Dbxref=GeneID:106605906,Genbank:XM_014202275.1;gbkey=mRNA;gene=LOC106605906;partial=true;product=lysyl oxidase homolog 3-like;transcript_id=XM_014202275.1\r\n",
      "NC_027300.1\tGnomon\texon\t896567\t896803\t.\t+\t.\tID=id117;Parent=rna21;Dbxref=GeneID:106607245,Genbank:XM_014204407.1;Note=The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: added 255 bases not found in genome assembly;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=manba;partial=true;product=mannosidase%2C beta A%2C lysosomal;transcript_id=XM_014204407.1\r\n",
      "NC_027300.1\tGnomon\texon\t936286\t936895\t.\t+\t.\tID=id137;Parent=rna23;Dbxref=GeneID:106610064,Genbank:XR_001329882.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X1;transcript_id=XR_001329882.1\r\n",
      "NC_027300.1\tGnomon\texon\t936286\t936895\t.\t+\t.\tID=id133;Parent=rna22;Dbxref=GeneID:106610064,Genbank:XR_001329921.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X2;transcript_id=XR_001329921.1\r\n",
      "NC_027300.1\tGnomon\texon\t936989\t937024\t.\t+\t.\tID=id138;Parent=rna23;Dbxref=GeneID:106610064,Genbank:XR_001329882.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X1;transcript_id=XR_001329882.1\r\n",
      "NC_027300.1\tGnomon\texon\t936989\t937024\t.\t+\t.\tID=id134;Parent=rna22;Dbxref=GeneID:106610064,Genbank:XR_001329921.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X2;transcript_id=XR_001329921.1\r\n",
      "NC_027300.1\tGnomon\texon\t937226\t937258\t.\t+\t.\tID=id140;Parent=rna24;Dbxref=GeneID:106610064,Genbank:XR_001329962.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X3;transcript_id=XR_001329962.1\r\n",
      "NC_027300.1\tGnomon\texon\t937417\t937478\t.\t+\t.\tID=id135;Parent=rna22;Dbxref=GeneID:106610064,Genbank:XR_001329921.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X2;transcript_id=XR_001329921.1\r\n",
      "NC_027300.1\tGnomon\texon\t937417\t937447\t.\t+\t.\tID=id141;Parent=rna24;Dbxref=GeneID:106610064,Genbank:XR_001329962.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X3;transcript_id=XR_001329962.1\r\n",
      "NC_027300.1\tGnomon\texon\t937417\t937487\t.\t+\t.\tID=id139;Parent=rna23;Dbxref=GeneID:106610064,Genbank:XR_001329882.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X1;transcript_id=XR_001329882.1\r\n",
      "NC_027300.1\tGnomon\texon\t937572\t937609\t.\t+\t.\tID=id136;Parent=rna22;Dbxref=GeneID:106610064,Genbank:XR_001329921.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X2;transcript_id=XR_001329921.1\r\n",
      "NC_027300.1\tGnomon\texon\t937811\t937943\t.\t+\t.\tID=id142;Parent=rna24;Dbxref=GeneID:106610064,Genbank:XR_001329962.1;gbkey=ncRNA;gene=LOC106610064;ncrna_class=lncRNA;product=uncharacterized LOC106610064%2C transcript variant X3;transcript_id=XR_001329962.1\r\n",
      "NC_027300.1\tGnomon\texon\t938153\t938273\t.\t+\t.\tID=id148;Parent=rna26;Dbxref=GeneID:106609218,Genbank:XR_001329767.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X3;transcript_id=XR_001329767.1\r\n",
      "NC_027300.1\tGnomon\texon\t938153\t938273\t.\t+\t.\tID=id153;Parent=rna27;Dbxref=GeneID:106609218,Genbank:XR_001329689.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X1;transcript_id=XR_001329689.1\r\n",
      "NC_027300.1\tGnomon\texon\t938153\t938273\t.\t+\t.\tID=id143;Parent=rna25;Dbxref=GeneID:106609218,Genbank:XR_001329715.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X2;transcript_id=XR_001329715.1\r\n",
      "NC_027300.1\tGnomon\texon\t938322\t938387\t.\t+\t.\tID=id144;Parent=rna25;Dbxref=GeneID:106609218,Genbank:XR_001329715.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X2;transcript_id=XR_001329715.1\r\n",
      "NC_027300.1\tGnomon\texon\t938322\t938387\t.\t+\t.\tID=id154;Parent=rna27;Dbxref=GeneID:106609218,Genbank:XR_001329689.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X1;transcript_id=XR_001329689.1\r\n",
      "NC_027300.1\tGnomon\texon\t938322\t938387\t.\t+\t.\tID=id149;Parent=rna26;Dbxref=GeneID:106609218,Genbank:XR_001329767.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X3;transcript_id=XR_001329767.1\r\n",
      "NC_027300.1\tGnomon\texon\t938419\t938600\t.\t+\t.\tID=id145;Parent=rna25;Dbxref=GeneID:106609218,Genbank:XR_001329715.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X2;transcript_id=XR_001329715.1\r\n",
      "NC_027300.1\tGnomon\texon\t938419\t938600\t.\t+\t.\tID=id155;Parent=rna27;Dbxref=GeneID:106609218,Genbank:XR_001329689.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X1;transcript_id=XR_001329689.1\r\n",
      "NC_027300.1\tGnomon\texon\t938419\t938600\t.\t+\t.\tID=id150;Parent=rna26;Dbxref=GeneID:106609218,Genbank:XR_001329767.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X3;transcript_id=XR_001329767.1\r\n",
      "NC_027300.1\tGnomon\texon\t938903\t939097\t.\t+\t.\tID=id156;Parent=rna27;Dbxref=GeneID:106609218,Genbank:XR_001329689.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X1;transcript_id=XR_001329689.1\r\n",
      "NC_027300.1\tGnomon\texon\t938903\t939036\t.\t+\t.\tID=id151;Parent=rna26;Dbxref=GeneID:106609218,Genbank:XR_001329767.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X3;transcript_id=XR_001329767.1\r\n",
      "NC_027300.1\tGnomon\texon\t938903\t938933\t.\t+\t.\tID=id146;Parent=rna25;Dbxref=GeneID:106609218,Genbank:XR_001329715.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X2;transcript_id=XR_001329715.1\r\n",
      "NC_027300.1\tGnomon\texon\t939610\t939738\t.\t+\t.\tID=id152;Parent=rna26;Dbxref=GeneID:106609218,Genbank:XR_001329767.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X3;transcript_id=XR_001329767.1\r\n",
      "NC_027300.1\tGnomon\texon\t940881\t941131\t.\t+\t.\tID=id147;Parent=rna25;Dbxref=GeneID:106609218,Genbank:XR_001329715.1;gbkey=ncRNA;gene=LOC106609218;ncrna_class=lncRNA;product=uncharacterized LOC106609218%2C transcript variant X2;transcript_id=XR_001329715.1\r\n",
      "NC_027300.1\tGnomon\texon\t969895\t969996\t.\t+\t.\tID=id157;Parent=rna28;Dbxref=GeneID:106607815,Genbank:XM_014205582.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X1;transcript_id=XM_014205582.1\r\n",
      "NC_027300.1\tGnomon\texon\t969895\t969996\t.\t+\t.\tID=id160;Parent=rna29;Dbxref=GeneID:106607815,Genbank:XM_014206352.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X2;transcript_id=XM_014206352.1\r\n",
      "NC_027300.1\tGnomon\texon\t970005\t970302\t.\t+\t.\tID=id162;Parent=rna30;Dbxref=GeneID:106607815,Genbank:XM_014206999.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X3;transcript_id=XM_014206999.1\r\n",
      "NC_027300.1\tGnomon\texon\t980119\t980127\t.\t+\t.\tID=id158;Parent=rna28;Dbxref=GeneID:106607815,Genbank:XM_014205582.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X1;transcript_id=XM_014205582.1\r\n",
      "NC_027300.1\tGnomon\texon\t980119\t980127\t.\t+\t.\tID=id161;Parent=rna29;Dbxref=GeneID:106607815,Genbank:XM_014206352.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X2;transcript_id=XM_014206352.1\r\n",
      "NC_027300.1\tGnomon\texon\t980800\t980979\t.\t+\t.\tID=id161;Parent=rna29;Dbxref=GeneID:106607815,Genbank:XM_014206352.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X2;transcript_id=XM_014206352.1\r\n",
      "NC_027300.1\tGnomon\texon\t980119\t980127\t.\t+\t.\tID=id163;Parent=rna30;Dbxref=GeneID:106607815,Genbank:XM_014206999.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X3;transcript_id=XM_014206999.1\r\n",
      "NC_027300.1\tGnomon\texon\t981034\t982290\t.\t+\t.\tID=id159;Parent=rna28;Dbxref=GeneID:106607815,Genbank:XM_014205582.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X1;transcript_id=XM_014205582.1\r\n",
      "NC_027300.1\tGnomon\texon\t981034\t982290\t.\t+\t.\tID=id164;Parent=rna30;Dbxref=GeneID:106607815,Genbank:XM_014206999.1;gbkey=mRNA;gene=LOC106607815;product=probable N-acetyltransferase CML1%2C transcript variant X3;transcript_id=XM_014206999.1\r\n",
      "NC_027300.1\tGnomon\texon\t1028250\t1028456\t.\t+\t.\tID=id183;Parent=rna34;Dbxref=GeneID:106610935,Genbank:XM_014212534.1;gbkey=mRNA;gene=LOC106610935;product=DNA-directed RNA polymerase II subunit RPB1-like%2C transcript variant X3;transcript_id=XM_014212534.1\r\n",
      "NC_027300.1\tGnomon\texon\t1028250\t1028456\t.\t+\t.\tID=id179;Parent=rna32;Dbxref=GeneID:106610935,Genbank:XM_014211027.1;gbkey=mRNA;gene=LOC106610935;product=DNA-directed RNA polymerase II subunit RPB1-like%2C transcript variant X1;transcript_id=XM_014211027.1\r\n",
      "NC_027300.1\tGnomon\texon\t1028250\t1028456\t.\t+\t.\tID=id181;Parent=rna33;Dbxref=GeneID:106610935,Genbank:XM_014211796.1;gbkey=mRNA;gene=LOC106610935;product=DNA-directed RNA polymerase II subunit RPB1-like%2C transcript variant X2;transcript_id=XM_014211796.1\r\n",
      "NC_027300.1\tGnomon\texon\t1029763\t1029968\t.\t+\t.\tID=id184;Parent=rna34;Dbxref=GeneID:106610935,Genbank:XM_014212534.1;gbkey=mRNA;gene=LOC106610935;product=DNA-directed RNA polymerase II subunit RPB1-like%2C transcript variant X3;transcript_id=XM_014212534.1\r\n",
      "NC_027300.1\tGnomon\texon\t1029763\t1029968\t.\t+\t.\tID=id182;Parent=rna33;Dbxref=GeneID:106610935,Genbank:XM_014211796.1;gbkey=mRNA;gene=LOC106610935;product=DNA-directed RNA polymerase II subunit RPB1-like%2C transcript variant X2;transcript_id=XM_014211796.1\r\n",
      "NC_027300.1\tGnomon\texon\t1029763\t1029968\t.\t+\t.\tID=id180;Parent=rna32;Dbxref=GeneID:106610935,Genbank:XM_014211027.1;gbkey=mRNA;gene=LOC106610935;product=DNA-directed RNA polymerase II subunit RPB1-like%2C transcript variant X1;transcript_id=XM_014211027.1\r\n",
      "NC_027300.1\tGnomon\texon\t1054148\t1054874\t.\t+\t.\tID=id178;Parent=rna31;Dbxref=GeneID:106606645,Genbank:XM_014203252.1;gbkey=mRNA;gene=LOC106606645;product=transcription factor SPT20 homolog;transcript_id=XM_014203252.1\r\n",
      "NC_027300.1\tGnomon\texon\t1072545\t1072745\t.\t-\t.\tID=id187;Parent=rna35;Dbxref=GeneID:106612287,Genbank:XM_014213686.1;gbkey=mRNA;gene=LOC106612287;product=neurofilament light polypeptide-like;transcript_id=XM_014213686.1\r\n",
      "NC_027300.1\tGnomon\texon\t1077884\t1078056\t.\t-\t.\tID=id185;Parent=rna35;Dbxref=GeneID:106612287,Genbank:XM_014213686.1;gbkey=mRNA;gene=LOC106612287;product=neurofilament light polypeptide-like;transcript_id=XM_014213686.1\r\n",
      "NC_027300.1\tGnomon\texon\t1092716\t1095465\t.\t-\t.\tID=id195;Parent=rna36;Dbxref=GeneID:106612874,Genbank:XM_014214912.1;gbkey=mRNA;gene=LOC106612874;product=lysyl oxidase homolog 3-like;transcript_id=XM_014214912.1\r\n",
      "NC_027300.1\tGnomon\texon\t1115385\t1115799\t.\t-\t.\tID=id188;Parent=rna36;Dbxref=GeneID:106612874,Genbank:XM_014214912.1;gbkey=mRNA;gene=LOC106612874;product=lysyl oxidase homolog 3-like;transcript_id=XM_014214912.1\r\n"
     ]
    }
   ],
   "source": [
    "!/Users/Shared/bioinformatics/bedtools2/bin/subtractBed \\\n",
    "-a ref_ICSASG_v2_top_level.exon.gff3 \\\n",
    "-b ref_ICSASG_v2_top_level.CDS.gff3 |\\\n",
    "head -100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#check if gene gff contains other sequence than mRNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!/Users/Shared/bioinformatics/bedtools2/bin/subtractBed \\\n",
    "-a ref_ICSASG_v2_top_level.gene.gff3 \\\n",
    "-b ref_ICSASG_v2_top_level.mRNA.gff3 |\\\n",
    "head -100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "## generate intron track "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!/Users/Shared/bioinformatics/bedtools2/bin/subtractBed \\\n",
    "-a ref_ICSASG_v2_top_level.gene.gff3 \\\n",
    "-b ref_ICSASG_v2_top_level.mRNA.gff3 \\\n",
    ">"
   ]
  }
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