{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extract _P.generosa_ BLAST results using gene IDs associated with methylation machinery.\n",
    "\n",
    "List of methylation machinery gene IDs comes from this GitHub Issue:\n",
    "\n",
    "- [https://github.com/RobertsLab/resources/issues/1116](https://github.com/RobertsLab/resources/issues/1116)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TODAY'S DATE:\n",
      "Fri Feb 26 11:36:59 PST 2021\n",
      "------------\n",
      "\n",
      "Distributor ID:\tUbuntu\n",
      "Description:\tUbuntu 20.04.2 LTS\n",
      "Release:\t20.04\n",
      "Codename:\tfocal\n",
      "\n",
      "------------\n",
      "HOSTNAME: \n",
      "computer\n",
      "\n",
      "------------\n",
      "Computer Specs:\n",
      "\n",
      "Architecture:                    x86_64\n",
      "CPU op-mode(s):                  32-bit, 64-bit\n",
      "Byte Order:                      Little Endian\n",
      "Address sizes:                   45 bits physical, 48 bits virtual\n",
      "CPU(s):                          8\n",
      "On-line CPU(s) list:             0-7\n",
      "Thread(s) per core:              1\n",
      "Core(s) per socket:              1\n",
      "Socket(s):                       8\n",
      "NUMA node(s):                    1\n",
      "Vendor ID:                       GenuineIntel\n",
      "CPU family:                      6\n",
      "Model:                           165\n",
      "Model name:                      Intel(R) Core(TM) i9-10885H CPU @ 2.40GHz\n",
      "Stepping:                        2\n",
      "CPU MHz:                         2399.998\n",
      "BogoMIPS:                        4799.99\n",
      "Hypervisor vendor:               VMware\n",
      "Virtualization type:             full\n",
      "L1d cache:                       256 KiB\n",
      "L1i cache:                       256 KiB\n",
      "L2 cache:                        2 MiB\n",
      "L3 cache:                        128 MiB\n",
      "NUMA node0 CPU(s):               0-7\n",
      "Vulnerability Itlb multihit:     KVM: Mitigation: VMX unsupported\n",
      "Vulnerability L1tf:              Not affected\n",
      "Vulnerability Mds:               Not affected\n",
      "Vulnerability Meltdown:          Not affected\n",
      "Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp\n",
      "Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization\n",
      "Vulnerability Spectre v2:        Mitigation; Enhanced IBRS, IBPB conditional, RSB filling\n",
      "Vulnerability Srbds:             Not affected\n",
      "Vulnerability Tsx async abort:   Not affected\n",
      "Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon nopl xtopology tsc_reliable nonstop_tsc cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced fsgsbase tsc_adjust bmi1 avx2 smep bmi2 invpcid rdseed adx smap clflushopt xsaveopt xsavec xgetbv1 xsaves arat pku ospke md_clear flush_l1d arch_capabilities\n",
      "\n",
      "------------\n",
      "\n",
      "Memory Specs\n",
      "\n",
      "              total        used        free      shared  buff/cache   available\n",
      "Mem:           53Gi       3.7Gi        42Gi       267Mi       7.2Gi        49Gi\n",
      "Swap:         2.0Gi          0B       2.0Gi\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "No LSB modules are available.\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "echo \"TODAY'S DATE:\"\n",
    "date\n",
    "echo \"------------\"\n",
    "echo \"\"\n",
    "#Display operating system info\n",
    "lsb_release -a\n",
    "echo \"\"\n",
    "echo \"------------\"\n",
    "echo \"HOSTNAME: \"; hostname \n",
    "echo \"\"\n",
    "echo \"------------\"\n",
    "echo \"Computer Specs:\"\n",
    "echo \"\"\n",
    "lscpu\n",
    "echo \"\"\n",
    "echo \"------------\"\n",
    "echo \"\"\n",
    "echo \"Memory Specs\"\n",
    "echo \"\"\n",
    "free -mh"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set variables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "env: data_dir=/home/samb/data/P_generosa\n",
      "env: genes_gff=/home/samb/data/P_generosa/Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "env: unique_pgen_match_IDs=/home/samb/data/P_generosa/20210219_pgen_methylation-machinery_gene-IDs.txt\n",
      "env: meth_machinery_list=/home/samb/data/P_generosa/20210219_methylation_list.txt\n",
      "env: results_table=/home/samb/data/P_generosa/20210222_pgen_methylation-machinery_BLAST-evals.tab\n"
     ]
    }
   ],
   "source": [
    "# Set data directories\n",
    "%env data_dir=/home/samb/data/P_generosa\n",
    "%env genes_gff=/home/samb/data/P_generosa/Panopea-generosa-vv0.74.a4.gene.gff3\n",
    "%env unique_pgen_match_IDs=/home/samb/data/P_generosa/20210219_pgen_methylation-machinery_gene-IDs.txt\n",
    "%env meth_machinery_list=/home/samb/data/P_generosa/20210219_methylation_list.txt\n",
    "%env results_table=/home/samb/data/P_generosa/20210222_pgen_methylation-machinery_BLAST-evals.tab\n",
    "data_dir=\"/home/samb/data/P_generosa\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/samb/data/P_generosa\n"
     ]
    }
   ],
   "source": [
    "cd {data_dir}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Download gene GFF, GFF checksums file, and GenSAS BLAST results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 14M\n",
      "-rw-rw-r-- 1 samb samb  147 Feb 19 10:59 20210219_methylation_list.txt\n",
      "-rw-rw-r-- 1 samb samb 1.5M Oct  3  2019 Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab\n",
      "-rw-rw-r-- 1 samb samb 1.3M Oct  3  2019 Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab\n",
      "-rw-rw-r-- 1 samb samb  11M Oct 14  2019 Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "-rw-rw-r-- 1 samb samb 6.0K Feb 19 20:33 checksums.md5\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "wget --quiet https://gannet.fish.washington.edu/Atumefaciens/20190928_Pgenerosa_v074.a4_gensas_annotation/Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab\n",
    "\n",
    "wget --quiet https://gannet.fish.washington.edu/Atumefaciens/20190928_Pgenerosa_v074.a4_gensas_annotation/Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab\n",
    "\n",
    "wget --quiet https://gannet.fish.washington.edu/Atumefaciens/20190928_Pgenerosa_v074.a4_gensas_annotation/checksums.md5\n",
    "\n",
    "wget --quiet https://gannet.fish.washington.edu/Atumefaciens/20190928_Pgenerosa_v074.a4_gensas_annotation/Panopea-generosa-vv0.74.a4.gene.gff3\n",
    "    \n",
    "ls -lh"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Inspect files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "-----------------------------------------------------------\n",
      "\n",
      "20210219_methylation_list.txt\n",
      "\n",
      "dnmt1\n",
      "dnmt3a\n",
      "dnmt3b\n",
      "dnmt3l\n",
      "mbd1\n",
      "mbd2\n",
      "mbd3\n",
      "mbd4\n",
      "mbd5\n",
      "mbd6\n",
      "mecp2\n",
      "Baz2a\n",
      "Baz2b\n",
      "UHRF1\n",
      "UHRF2\n",
      "\n",
      "\n",
      "-----------------------------------------------------------\n",
      "\n",
      "Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab\n",
      "\n",
      "#\n",
      "# Output is generated by GenSAS 7.x-5.0\n",
      "#\n",
      "#name     : mRNA\n",
      "#start    : Start of alignment in subject\n",
      "#end      : End of alignment in subject\n",
      "#m_start  : Start of alignment in query\n",
      "#m_end    : End of alignment in query\n",
      "#al       : Alignment length\n",
      "#score    : Row score of the match\n",
      "#evalue   : E value of the match\n",
      "#identity : Percentage of identical matches\n",
      "mame\tstart\tend\tscore\tAccession\tMatch ID\tm_start\tm_end\tE-value\tidentity\tal\n",
      "21910-PGEN_.00g000010.m01\t121\t229\t165\tQ86IC9\tsp|Q86IC9|CAMT1_DICDI\t11\t122\t8.93e-14\t35.652\t115\n",
      "21910-PGEN_.00g000020.m01\t147\t467\t968\tP04177\tsp|P04177|TY3H_RAT\t20\t339\t3.47e-127\t55.140\t321\n",
      "\n",
      "\n",
      "-----------------------------------------------------------\n",
      "\n",
      "Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab\n",
      "\n",
      "#\n",
      "# Output is generated by GenSAS 7.x-5.0\n",
      "#\n",
      "#name     : mRNA\n",
      "#start    : Start of alignment in subject\n",
      "#end      : End of alignment in subject\n",
      "#m_start  : Start of alignment in query\n",
      "#m_end    : End of alignment in query\n",
      "#al       : Alignment length\n",
      "#score    : Row score of the match\n",
      "#evalue   : E value of the match\n",
      "#identity : Percentage of identical matches\n",
      "mame\tstart\tend\tscore\tAccession\tMatch ID\tm_start\tm_end\tE-value\tidentity\tal\n",
      "21910-PGEN_.00g000020.m01\t147\t467\t945\tP04177\tsp|P04177|TY3H_RAT\t20\t339\t7.9e-101\t55.1\t321\n",
      "21910-PGEN_.00g000050.m01\t566\t722\t180\tQ8L840\tsp|Q8L840|RQL4A_ARATH\t2\t167\t2.4e-12\t35.1\t168\n",
      "\n",
      "\n",
      "-----------------------------------------------------------\n",
      "\n",
      "Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "\n",
      "##gff-version 3\n",
      "##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM\n",
      "##Project Name : Pgenerosa_v074\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t2\t4719\t.\t+\t.\tID=PGEN_.00g000010;Name=PGEN_.00g000010;original_ID=21510-PGEN_.00g234140;Alias=21510-PGEN_.00g234140;original_name=21510-PGEN_.00g234140;Notes=sp|Q86IC9|CAMT1_DICDI [BLAST protein vs protein (blastp) 2.7.1],PF01596.12 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t19808\t36739\t.\t-\t.\tID=PGEN_.00g000020;Name=PGEN_.00g000020;original_ID=21510-PGEN_.00g234150;Alias=21510-PGEN_.00g234150;original_name=21510-PGEN_.00g234150;Notes=sp|P04177|TY3H_RAT [BLAST protein vs protein (blastp) 2.7.1],sp|P04177|TY3H_RAT [DIAMOND Functional 0.9.22],IPR036951 [InterProScan 5.29-68.0],PF00351.16 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t49248\t52578\t.\t-\t.\tID=PGEN_.00g000030;Name=PGEN_.00g000030;original_ID=21510-PGEN_.00g234160;Alias=21510-PGEN_.00g234160;original_name=21510-PGEN_.00g234160;Notes=PF08054.6 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t55792\t67546\t.\t+\t.\tID=PGEN_.00g000040;Name=PGEN_.00g000040;original_ID=21510-PGEN_.00g234170;Alias=21510-PGEN_.00g234170;original_name=21510-PGEN_.00g234170\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t67586\t69113\t.\t-\t.\tID=PGEN_.00g000050;Name=PGEN_.00g000050;original_ID=21510-PGEN_.00g234180;Alias=21510-PGEN_.00g234180;original_name=21510-PGEN_.00g234180;Notes=sp|Q8L840|RQL4A_ARATH [BLAST protein vs protein (blastp) 2.7.1],sp|Q8L840|RQL4A_ARATH [DIAMOND Functional 0.9.22],PF00270.24 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t70713\t81099\t.\t+\t.\tID=PGEN_.00g000060;Name=PGEN_.00g000060;original_ID=21510-PGEN_.00g234190;Alias=21510-PGEN_.00g234190;original_name=21510-PGEN_.00g234190;Notes=sp|Q61043|NIN_MOUSE [DIAMOND Functional 0.9.22],PF04443.7 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t183686\t186073\t.\t+\t.\tID=PGEN_.00g000070;Name=PGEN_.00g000070;original_ID=21510-PGEN_.00g234200;Alias=21510-PGEN_.00g234200;original_name=21510-PGEN_.00g234200;Notes=PF15364.1 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t187328\t188353\t.\t+\t.\tID=PGEN_.00g000080;Name=PGEN_.00g000080;original_ID=21510-PGEN_.00g234210;Alias=21510-PGEN_.00g234210;original_name=21510-PGEN_.00g234210;Notes=sp|A1E2V0|BIRC3_CANLF [BLAST protein vs protein (blastp) 2.7.1],sp|Q24307|DIAP2_DROME [DIAMOND Functional 0.9.22],IPR001370 [InterProScan 5.29-68.0],PF02229.11 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t189849\t190460\t.\t-\t.\tID=PGEN_.00g000090;Name=PGEN_.00g000090;original_ID=21510-PGEN_.00g234220;Alias=21510-PGEN_.00g234220;original_name=21510-PGEN_.00g234220;Notes=sp|P34456|YMD2_CAEEL [BLAST protein vs protein (blastp) 2.7.1],PF10284.4 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t191069\t191410\t.\t-\t.\tID=PGEN_.00g000100;Name=PGEN_.00g000100;original_ID=21510-PGEN_.00g234230;Alias=21510-PGEN_.00g234230;original_name=21510-PGEN_.00g234230;Notes=PF10228.4 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t191836\t192282\t.\t-\t.\tID=PGEN_.00g000110;Name=PGEN_.00g000110;original_ID=21510-PGEN_.00g234240;Alias=21510-PGEN_.00g234240;original_name=21510-PGEN_.00g234240;Notes=IPR009044 [InterProScan 5.29-68.0],PF02229.11 [Pfam 1.6]\n",
      "PGA_scaffold1__77_contigs__length_89643857\tGenSAS_5d9637f372b5d-publish\tgene\t192526\t193324\t.\t-\t.\tID=PGEN_.00g000120;Name=PGEN_.00g000120;original_ID=21510-PGEN_.00g234250;Alias=21510-PGEN_.00g234250;original_name=21510-PGEN_.00g234250;Notes=sp|P34457|YMD3_CAEEL [DIAMOND Functional 0.9.22],IPR036397 [InterProScan 5.29-68.0],PF13276.1 [Pfam 1.6]\n",
      "\n",
      "\n",
      "-----------------------------------------------------------\n",
      "\n",
      "checksums.md5\n",
      "\n",
      "fb0ed4cf6af7adaa6579da118a887cb9  ./Panopea-generosa-vv0.74.a4.5d82b23f69545-braker.genes.gff3\n",
      "aed6dae0cc90216f8606077c1927e6ff  ./Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.CDS.fna\n",
      "4b3369aa246cb179ecf374f5c4f38966  ./Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.genes.fna\n",
      "f0afd89f974e81fcbadef8cae13423d9  ./Panopea-generosa-vv0.74.a4.5d82b316cd298-trnascan.tRNA.fna\n",
      "36fbf825ef85893cc6256f2dcc2b86c2  ./Panopea-generosa-vv0.74.a4.5d82b316cd298-trnascan.tRNA.gff3\n",
      "8f11ea587217243e02568aec3c59d78c  ./Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.CDS.fna\n",
      "8401b6372774f594f8aad52d0aa5a1d6  ./Panopea-generosa-vv0.74.a4.rRNA.gff3\n",
      "acd5a79a0879f602815ace545faedab7  ./Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.protein.faa\n",
      "4f751f896347e96241daf6006d3a3abe  ./Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.protein.faa\n",
      "7c348d72a890232bd09676e38d6b8ada  ./Panopea-generosa-vv0.74.a4.gene.gff3\n",
      "a0a5cbd449cf90e8b91a188504e76f8c  ./Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.CDS.fna\n",
      "965b78b7ebb3274edb8bab0ca1e0e8c1  ./Panopea-generosa-vv0.74.a4.5d250896def4c-repeatmasker.repeats.gff3\n",
      "14d207d90085eeac0002ba8cdf7ca3aa  ./Panopea-generosa-vv0.74.a4.CDS.gff3\n",
      "c37fa754433cdab8d609efb0f90a83fe  ./Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab\n",
      "d36db1a170b0f037287af6fbfe0b45dd  ./Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.genes.gff3\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "line=\"-----------------------------------------------------------\"\n",
    "for file in *\n",
    "do\n",
    "    echo \"\"\n",
    "    echo \"${line}\"\n",
    "    echo \"\"\n",
    "    echo \"${file}\"\n",
    "    echo \"\"\n",
    "    head -n 15 \"${file}\"\n",
    "    echo \"\"\n",
    "done\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Verify GFF checksum"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "diff <(md5sum Panopea-generosa-vv0.74.a4.gene.gff3 | cut -d \" \" -f1) <(grep \"Panopea-generosa-vv0.74.a4.gene.gff3\" checksums.md5 | cut -d \" \" -f1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## List of _P.generosa_ matching gene IDs from methylation machinery list file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PGEN_.00g104080\tBaz2b\n",
      "PGEN_.00g104170\tBaz2b\n",
      "PGEN_.00g116950\tmbd5\n",
      "PGEN_.00g186870\tctcf\n",
      "PGEN_.00g192900\tUHRF1\n",
      "PGEN_.00g202750\tmbd2\n",
      "PGEN_.00g209890\tmbd2\n",
      "PGEN_.00g209900\tmbd4\n",
      "PGEN_.00g243700\tegr1\n",
      "PGEN_.00g249090\tegr1\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "# Pull out unique list of pgen IDs matching methylation machinery list\n",
    "while read -r line\n",
    "do\n",
    "\n",
    "  # Test for empty line\n",
    "  [ -z ${line} ] && { echo \"Empty line found in ${meth_machinery_list}.\"; exit 1; }\n",
    "\n",
    "  # Search GFF for methylation gene name\n",
    "  if grep --quiet --ignore-case \"|${line}\" \"${genes_gff}\"; then\n",
    "\n",
    "    # Loop through matches, in case of multiple matches\n",
    "    for match in $(grep --ignore-case \"|${line}\" \"${genes_gff}\" | awk -F'[=;]' '{print $2}')\n",
    "    do\n",
    "      # Print tab-delimited results\n",
    "      printf \"%s\\t%s\\n\" \"${match}\" \"${line}\"\n",
    "    done\n",
    "  fi\n",
    "\n",
    "done < ${meth_machinery_list} | sort -k1,1 -u >> ${unique_pgen_match_IDs}\n",
    "\n",
    "head ${unique_pgen_match_IDs}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Search BLAST tables for gene IDs and print to tab-delimited file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "printf \"%s\\t%s\\t%s\\t%s\\n\" \"Gene_ID\" \"gene_name\" \"BLASTp_evalue\" \"DIAMOND_evalue\" > ${results_table}\n",
    "while read -r pgen_ID meth_machinery\n",
    "do\n",
    "  blastp=$(grep \"${pgen_ID}\" Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab | head -n 1 | cut -f9)\n",
    "  diamond=$(grep \"${pgen_ID}\" Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab | head -n 1 | cut -f9)\n",
    "  printf \"%s\\t%s\\t%s\\t%s\\n\" \"${pgen_ID}\" \"${meth_machinery}\" \"${blastp}\" \"${diamond}\"\n",
    "done < ${unique_pgen_match_IDs} >> ${results_table}\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Gene_ID          gene_name  BLASTp_evalue  DIAMOND_evalue\n",
      "PGEN_.00g104080  Baz2b      1.05e-98       5.4e-102\n",
      "PGEN_.00g104170  Baz2b      3.09e-96       1.2e-109\n",
      "PGEN_.00g116950  mbd5       6.40e-21       2.8e-20\n",
      "PGEN_.00g186870  ctcf       1.25e-116\n",
      "PGEN_.00g192900  UHRF1      2.32e-19\n",
      "PGEN_.00g202750  mbd2       9.46e-82       2.6e-63\n",
      "PGEN_.00g209890  mbd2       4.37e-19       9.2e-09\n",
      "PGEN_.00g209900  mbd4       3.14e-32       8.0e-29\n",
      "PGEN_.00g243700  egr1       6.24e-58       2.2e-23\n",
      "PGEN_.00g249090  egr1       4.19e-18       2.6e-06\n",
      "PGEN_.00g283000  dnmt1      5.03e-10\n",
      "PGEN_.00g283010  dnmt1      0.0            7.3e-224\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cat ${results_table} | column -t"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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