{
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   "metadata": {},
   "source": [
    "Aspen Coyle, afcoyle@uw.edu\n",
    "\n",
    "2021/03/20\n",
    "\n",
    "Roberts lab at SAFS\n",
    "\n",
    "### Removing duplicate lines from genes\n",
    "\n",
    "Completed getting all our GO terms! Now, time to get input for GO-MWU.\n",
    "We need 2 tables:\n",
    "- A 2-column table of genes and GO terms\n",
    "- A 2-column table of genes and log2 fold change without repeated genes\n",
    "\n",
    "The table of genes and log2 fold change is created using R in the script 11_2_prod_cluster_GOterms.Rmd\n",
    "In getting GO terms, we made a 2-col tab-separated table of genes and GO terms.\n",
    "Now we need to eliminate all repeated genes. To do this, we'll use the nrify_GOtable.pl script. \n",
    "This can be found in the [GitHub repo for GO-MWU](https://github.com/z0on/GO_MWU)\n",
    "\n",
    "We'll put these files in a subdirectory within the scripts directory, as this is what GO-MWU calls for. All GO-MWU files are also within that directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/mnt/c/Users/acoyl/Documents/GitHub/hemat_bairdi_transcriptome/scripts'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## All Samples"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Eliminate gene repeats, concatenate GO terms for cbai_v2.0, all samples, blue module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/all_crabs_blue_GOIDs.txt > 11_4_running_GOMWU/cbai2.0_all_crabs_blue_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1803 11_4_running_GOMWU/cbai2.0_all_crabs_blue_module_GOIDs_norepeats.txt\n"
     ]
    }
   ],
   "source": [
    "# See length of file without repeats\n",
    "!wc -l 11_4_running_GOMWU/cbai2.0_all_crabs_blue_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1803\n"
     ]
    }
   ],
   "source": [
    "# Manually see how many repeats we have - looks indentical, script running properly\n",
    "!sort ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/all_crabs_blue_GOIDs.txt | uniq | wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with cbai_v2.0, all samples, cyan module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/all_crabs_cyan_GOIDs.txt > 11_4_running_GOMWU/cbai2.0_all_crabs_cyan_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with cbai_v2.0, all samples, salmon module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/all_crabs_salmon_GOIDs.txt > 11_4_running_GOMWU/cbai2.0_all_crabs_salmon_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with cbai_v2.0, all samples, yellow module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/all_crabs_yellow_GOIDs.txt > 11_4_running_GOMWU/cbai2.0_all_crabs_yellow_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with cbai_v4.0, all samples, brown module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev4.0/all_crabs_brown_GOIDs.txt > 11_4_running_GOMWU/cbai4.0_all_crabs_brown_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with cbai_v4.0, all samples, black module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev4.0/all_crabs_black_GOIDs.txt > 11_4_running_GOMWU/cbai4.0_all_crabs_black_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with hemat_v1.6, all samples, brown module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/hemat_transcriptomev1.6/all_crabs_brown_GOIDs.txt > 11_4_running_GOMWU/hemat1.6_all_crabs_brown_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with hemat_v1.6, all samples, pink module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/hemat_transcriptomev1.6/all_crabs_pink_GOIDs.txt > 11_4_running_GOMWU/hemat1.6_all_crabs_pink_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Ambient and Lowered-temp Samples\n",
    "\n",
    "As described in earlier scripts (check 11_1), the WGCNA run on these samples was explicitly to look at change in _Hematodinium_ level over time, and thus excluded elevated-temp samples (for which only one timepoint with qPCR data is available per crab)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Eliminate gene repeats, concatenate GO terms for cbai_v2.0, amb+low samples, blue module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/amb_low_blue_GOIDs.txt > 11_4_running_GOMWU/cbai2.0_amb_low_blue_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1659 11_4_running_GOMWU/cbai2.0_amb_low_blue_module_GOIDs_norepeats.txt\n"
     ]
    }
   ],
   "source": [
    "# See length of file without repeats\n",
    "!wc -l 11_4_running_GOMWU/cbai2.0_amb_low_blue_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1659\n"
     ]
    }
   ],
   "source": [
    "# Manually see how many repeats we have - looks indentical, script running properly\n",
    "!sort ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev2.0/amb_low_blue_GOIDs.txt | uniq | wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with cbai_v4.0, amb + low, red module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/cbai_transcriptomev4.0/amb_low_red_GOIDs.txt > 11_4_running_GOMWU/cbai4.0_amb_low_red_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Continue with hemat_v1.6.0, amb + low, green module\n",
    "!11_4_running_GOMWU/./nrify_GOtable.pl ../output/accession_n_GOids/WGCNA_modules/hemat_transcriptomev1.6/amb_low_green_GOIDs.txt > 11_4_running_GOMWU/hemat1.6_amb_low_green_module_GOIDs_norepeats.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Well done! Each comparison should now have both inputs needed for GOMWU"
   ]
  }
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