notebooks/30_Mupexi_cleanup.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "toc": true
   },
   "source": [
    "<h1>Table of Contents<span class=\"tocSkip\"></span></h1>\n",
    "<div class=\"toc\"><ul class=\"toc-item\"><li><span><a href=\"#Dependencies\" data-toc-modified-id=\"Dependencies-1\">Dependencies</a></span></li><li><span><a href=\"#Functions\" data-toc-modified-id=\"Functions-2\">Functions</a></span></li><li><span><a href=\"#Paths\" data-toc-modified-id=\"Paths-3\">Paths</a></span></li><li><span><a href=\"#Main\" data-toc-modified-id=\"Main-4\">Main</a></span><ul class=\"toc-item\"><li><span><a href=\"#CBTTC\" data-toc-modified-id=\"CBTTC-4.1\">CBTTC</a></span></li><li><span><a href=\"#Clean-up-mupexi-files-to-include-mutations-that-are-overlapped-from-strelka-and-mutect2-for-cbttc\" data-toc-modified-id=\"Clean-up-mupexi-files-to-include-mutations-that-are-overlapped-from-strelka-and-mutect2-for-cbttc-4.2\">Clean up mupexi files to include mutations that are overlapped from strelka and mutect2 for cbttc</a></span></li><li><span><a href=\"#TARGET\" data-toc-modified-id=\"TARGET-4.3\">TARGET</a></span></li></ul></li></ul></div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Dependencies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "library(maftools)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Functions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Paths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "manifestpath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Manifests/\"\n",
    "datapath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/\"\n",
    "plotpath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Plots/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Main"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "load(file = paste0(datapath,\"snv/total_mut_manifest_estimate.RData\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## CBTTC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_mafsummary <- read.table(file = paste0(datapath, \"snv/CBTTC_mafsummary_overlapped_3VAF.txt\"),\n",
    "                        sep = \"\\t\", check.names = F,\n",
    "                        header = TRUE, stringsAsFactors = FALSE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "mymaf_CBTTC <- read.maf(maf =  paste0(datapath, \"snv/CBTTC_maf_overlapped_3VAF.maf\"),\n",
    "                      useAll = TRUE, verbose = FALSE,\n",
    "                      vc_nonSyn = c(\"Frame_Shift_Del\", \"Frame_Shift_Ins\", \n",
    "                                    \"Nonsense_Mutation\",\"Nonstop_Mutation\", \n",
    "                                    \"In_Frame_Del\",\"In_Frame_Ins\", \n",
    "                                    \"Missense_Mutation\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_data_maf <- mymaf_CBTTC@data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_data_maf$Tumor_Sample_Barcode <- as.character(CBTTC_data_maf$Tumor_Sample_Barcode)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Add sample id to maf file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_data_maf_sampleid <- merge(CBTTC_mafsummary[,c(\"sample_id\", \"Tumor_Sample_Barcode\")], \n",
    "                                 CBTTC_data_maf, by = \"Tumor_Sample_Barcode\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "796"
      ],
      "text/latex": [
       "796"
      ],
      "text/markdown": [
       "796"
      ],
      "text/plain": [
       "[1] 796"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(unique(CBTTC_data_maf_sampleid$Tumor_Sample_Barcode))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "subset to samples included in total_mut_manifest_estimate_quanti"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>'CBTTC_data_maf'</li><li>'CBTTC_data_maf_sampleid'</li><li>'CBTTC_mafsummary'</li><li>'datapath'</li><li>'manifestpath'</li><li>'mymaf_CBTTC'</li><li>'plotpath'</li><li>'total_mut_manifest_estimate'</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'CBTTC\\_data\\_maf'\n",
       "\\item 'CBTTC\\_data\\_maf\\_sampleid'\n",
       "\\item 'CBTTC\\_mafsummary'\n",
       "\\item 'datapath'\n",
       "\\item 'manifestpath'\n",
       "\\item 'mymaf\\_CBTTC'\n",
       "\\item 'plotpath'\n",
       "\\item 'total\\_mut\\_manifest\\_estimate'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'CBTTC_data_maf'\n",
       "2. 'CBTTC_data_maf_sampleid'\n",
       "3. 'CBTTC_mafsummary'\n",
       "4. 'datapath'\n",
       "5. 'manifestpath'\n",
       "6. 'mymaf_CBTTC'\n",
       "7. 'plotpath'\n",
       "8. 'total_mut_manifest_estimate'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] \"CBTTC_data_maf\"              \"CBTTC_data_maf_sampleid\"    \n",
       "[3] \"CBTTC_mafsummary\"            \"datapath\"                   \n",
       "[5] \"manifestpath\"                \"mymaf_CBTTC\"                \n",
       "[7] \"plotpath\"                    \"total_mut_manifest_estimate\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ls()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_data_maf <- CBTTC_data_maf_sampleid[CBTTC_data_maf_sampleid$sample_id %in% total_mut_manifest_estimate$sample_id,]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>'7316-2558'</li><li>'7316-3299'</li><li>'7316-3299'</li><li>'7316-3299'</li><li>'7316-3299'</li><li>'7316-3299'</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item '7316-2558'\n",
       "\\item '7316-3299'\n",
       "\\item '7316-3299'\n",
       "\\item '7316-3299'\n",
       "\\item '7316-3299'\n",
       "\\item '7316-3299'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. '7316-2558'\n",
       "2. '7316-3299'\n",
       "3. '7316-3299'\n",
       "4. '7316-3299'\n",
       "5. '7316-3299'\n",
       "6. '7316-3299'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] \"7316-2558\" \"7316-3299\" \"7316-3299\" \"7316-3299\" \"7316-3299\" \"7316-3299\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(CBTTC_data_maf$sample_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "470"
      ],
      "text/latex": [
       "470"
      ],
      "text/markdown": [
       "470"
      ],
      "text/plain": [
       "[1] 470"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(unique(CBTTC_data_maf$Tumor_Sample_Barcode))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Clean up mupexi files to include mutations that are overlapped from strelka and mutect2 for cbttc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "CBTTC manifest that optitype and mutect2 vcf files are matched with sample ids and all. Use this to map mupexi filenames to sample_id"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "opti_mutect2_cbttc <- read.table(file = paste0(manifestpath, \"mutect2_optitype_manifest_cbttc.txt\"),\n",
    "                        sep = \"\\t\", check.names = F, \n",
    "                        header = TRUE, stringsAsFactors = FALSE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>512</li><li>66</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 512\n",
       "\\item 66\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 512\n",
       "2. 66\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 512  66"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(opti_mutect2_cbttc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>'b5a7b96d-940c-475a-a439-32b898026903.recode.vcf'</li><li>'9ce2828c-bbcf-4112-a4cb-95cc69c72c81.recode.vcf'</li><li>'aa08d3dd-3ba7-4852-8929-eaa68c1e5856.recode.vcf'</li><li>'bd321ccc-ce04-4164-91fb-676105eef65e.recode.vcf'</li><li>'e31d632e-7cff-41de-b4da-57f5bf53a5c8.recode.vcf'</li><li>'d9eaced6-2f46-4876-90cd-3c2ff990615e.recode.vcf'</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'b5a7b96d-940c-475a-a439-32b898026903.recode.vcf'\n",
       "\\item '9ce2828c-bbcf-4112-a4cb-95cc69c72c81.recode.vcf'\n",
       "\\item 'aa08d3dd-3ba7-4852-8929-eaa68c1e5856.recode.vcf'\n",
       "\\item 'bd321ccc-ce04-4164-91fb-676105eef65e.recode.vcf'\n",
       "\\item 'e31d632e-7cff-41de-b4da-57f5bf53a5c8.recode.vcf'\n",
       "\\item 'd9eaced6-2f46-4876-90cd-3c2ff990615e.recode.vcf'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'b5a7b96d-940c-475a-a439-32b898026903.recode.vcf'\n",
       "2. '9ce2828c-bbcf-4112-a4cb-95cc69c72c81.recode.vcf'\n",
       "3. 'aa08d3dd-3ba7-4852-8929-eaa68c1e5856.recode.vcf'\n",
       "4. 'bd321ccc-ce04-4164-91fb-676105eef65e.recode.vcf'\n",
       "5. 'e31d632e-7cff-41de-b4da-57f5bf53a5c8.recode.vcf'\n",
       "6. 'd9eaced6-2f46-4876-90cd-3c2ff990615e.recode.vcf'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] \"b5a7b96d-940c-475a-a439-32b898026903.recode.vcf\"\n",
       "[2] \"9ce2828c-bbcf-4112-a4cb-95cc69c72c81.recode.vcf\"\n",
       "[3] \"aa08d3dd-3ba7-4852-8929-eaa68c1e5856.recode.vcf\"\n",
       "[4] \"bd321ccc-ce04-4164-91fb-676105eef65e.recode.vcf\"\n",
       "[5] \"e31d632e-7cff-41de-b4da-57f5bf53a5c8.recode.vcf\"\n",
       "[6] \"d9eaced6-2f46-4876-90cd-3c2ff990615e.recode.vcf\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(opti_mutect2_cbttc$name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/'"
      ],
      "text/latex": [
       "'/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/'"
      ],
      "text/markdown": [
       "'/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/'"
      ],
      "text/plain": [
       "[1] \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "datapath"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "mountpath <- \"/Users/anabbi/Desktop/H4H/immpedcan/antigen_prediction/output/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "flelist <- list.files(mountpath, pattern = \"mupexi\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "603"
      ],
      "text/latex": [
       "603"
      ],
      "text/markdown": [
       "603"
      ],
      "text/plain": [
       "[1] 603"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(flelist)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "470"
      ],
      "text/latex": [
       "470"
      ],
      "text/markdown": [
       "470"
      ],
      "text/plain": [
       "[1] 470"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(unique(CBTTC_data_maf$sample_id))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"00267954-7696-4d50-b48b-75d0ae76dafc.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"00382118-5ea5-447b-9ec3-b36ad8d2a2f7.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"0062aa93-2238-46cc-82fb-a4a1fe8eb19e.mupexi\"\n",
      "[1] \"0167ee47-7441-4965-8cd8-c7b607fcca22.mupexi\"\n",
      "[1] \"01a07f01-2f87-4b88-9aeb-d2bffdb75a24.mupexi\"\n",
      "[1] \"01c6d153-7b01-418a-be36-4f0dbee5e85c.mupexi\"\n",
      "[1] \"041816ac-abd8-4f4a-af58-4b186bd5dc03.mupexi\"\n",
      "[1] \"0436934f-3c8f-490e-bba8-f04ac7dcb58c.mupexi\"\n",
      "[1] \"0449d846-0d30-4749-95e0-51085f07a4ed.mupexi\"\n",
      "[1] \"04b96cbf-d1c2-434a-ab0e-0b2931414964.mupexi\"\n",
      "[1] \"053dac4d-c91e-457b-8194-6272e0affeba.mupexi\"\n",
      "[1] \"05c2f817-353b-45af-b386-8214339d498f.mupexi\"\n",
      "[1] \"074c52e2-5774-4695-8e0c-78e3b3856457.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"08366cf8-3bfe-477a-9819-f50949cda8b3.mupexi\"\n",
      "[1] \"088b27bd-d952-4b81-9978-b3da0392c5dc.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"088de9c9-b8b8-4943-896a-0b13b2aa387a.mupexi\"\n"
     ]
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     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"089b5063-561c-46e2-82c4-21d0ed283720.mupexi\"\n",
      "[1] \"093584ea-a64b-4031-828c-3ff0a82bfeb4.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"09b73206-ab2a-4295-9e66-789e6a6d745f.mupexi\"\n",
      "[1] \"0a54bd69-84a2-499f-8349-cd028da812d3.mupexi\"\n",
      "[1] \"0a6274e8-dbd3-4c58-9482-988c2226cd64.mupexi\"\n",
      "[1] \"0aeac7e6-075e-433d-8482-a41a257af3c0.mupexi\"\n",
      "[1] \"0b91a297-a087-4265-b0ad-f5f3558b3ba8.mupexi\"\n",
      "[1] \"0b9c2ce2-cbb1-4a84-88d1-f85288d0e7b7.mupexi\"\n",
      "[1] \"0bca1517-31a1-4d75-8b9b-f48479826ba7.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"0cc7ffd6-3f34-46ea-b00b-08a29904c574.mupexi\"\n"
     ]
    },
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      "[1] \"e4fb74e7-f5c4-4835-bd66-4cee9f1e4284.mupexi\"\n"
     ]
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    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"e52bf57c-f90a-4717-b405-a5c54ba06bd8.mupexi\"\n"
     ]
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     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"e53badfd-c0a9-432e-bc67-bac15cfd6916.mupexi\"\n"
     ]
    },
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     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"e554b9be-3e1e-4a7d-ac4d-a331ad6956a1.mupexi\"\n",
      "[1] \"e55f58f0-f3a3-4088-a136-00071cfb21fc.mupexi\"\n"
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      "sample_id not found\n",
      "\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"e61923c5-301a-47bf-9c7e-1c5c6a1b59fc.mupexi\"\n",
      "[1] \"e64997e0-50a9-47f8-8520-588e382aa6af.mupexi\"\n"
     ]
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    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"e6a22574-fa09-4bbf-ad7a-10074bb1919c.mupexi\"\n",
      "[1] \"e6bd2790-847d-4c83-bd42-4f12e2d4dc6a.mupexi\"\n",
      "[1] \"e74f64b7-656a-42a0-aec7-2bd35a2f170e.mupexi\"\n",
      "[1] \"e75edc5a-5d46-4fb8-b383-e0eae17c1326.mupexi\"\n",
      "[1] \"e775dedf-1521-43cc-9ef0-4c8cbb38b60c.mupexi\"\n",
      "[1] \"e7c74465-3a8f-416b-97c8-ce58ceeec6fa.mupexi\"\n",
      "[1] \"e816d8eb-e949-47be-82b5-9f7fd5d7b559.mupexi\"\n",
      "[1] \"e83013ac-a640-45e4-981e-dd5e13ee612f.mupexi\"\n",
      "[1] \"e8391c47-b957-484b-b17f-cc2d1da46cf4.mupexi\"\n",
      "[1] \"e92efabc-a825-4d18-9fab-014853cd153d.mupexi\"\n",
      "[1] \"e9330f7e-0100-4dbb-8753-b6038fa47dd6.mupexi\"\n",
      "[1] \"e9d3b8d4-be3e-4a76-bc14-0344542f940d.mupexi\"\n",
      "[1] \"ea03ec9a-d391-42d2-866a-719c0890c566.mupexi\"\n",
      "[1] \"eb94601f-023b-4b30-a6e1-b357e1ddc832.mupexi\"\n",
      "[1] \"eb9b21c3-1791-4b46-b0ab-44ded4cd7a8c.mupexi\"\n",
      "[1] \"ebd8b66b-5ada-4f42-8c2c-e93d5659b208.mupexi\"\n"
     ]
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    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"ebf19160-2d88-4cf1-8001-352135979dbe.mupexi\"\n",
      "[1] \"ec3f136b-bb48-48b0-a5d0-5980d1078114.mupexi\"\n",
      "[1] \"ecde4d12-4c42-4e79-8a97-9ba516041f65.mupexi\"\n",
      "[1] \"ed17c15e-d3a9-4e36-ae3b-42fc4a651f4f.mupexi\"\n",
      "[1] \"ee598133-2ae4-4cbe-b8cc-3ece3b1e3c37.mupexi\"\n",
      "[1] \"ef9607f9-f44e-41c4-be97-359a869a5873.mupexi\"\n",
      "[1] \"ef9bef68-c95d-43b2-863a-0b87b673e52d.mupexi\"\n",
      "[1] \"f03ab402-4e8d-4d91-a5bc-71f024f3b819.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"f106ff41-1d3c-4342-b70e-353d9a8030df.mupexi\"\n",
      "[1] \"f14efeb6-2055-47a4-bc66-f42a51a507f9.mupexi\"\n",
      "[1] \"f15fcecc-01cd-4085-9aaf-19d55bd2170e.mupexi\"\n",
      "[1] \"f1a6dcb3-fcb6-4941-b2c0-3301e0839e24.mupexi\"\n",
      "[1] \"f3ac9f84-b9d8-4db3-9ffd-22bbab251aba.mupexi\"\n",
      "[1] \"f3db6565-8ade-4a3f-8e3f-9114910b9858.mupexi\"\n",
      "[1] \"f44e3994-0339-4c32-a221-a82df3977c79.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Genes in mupexi not found in overlapped variants\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"f482ccb7-1817-4ad1-8cce-0df4daee353b.mupexi\"\n",
      "[1] \"f4c1b1c1-5e9e-4caa-8251-469534c1d812.mupexi\"\n",
      "[1] \"f4da6550-79e9-4fc7-9553-276274f06d15.mupexi\"\n",
      "[1] \"f5557242-1e92-4209-9b48-38fc7333346e.mupexi\"\n",
      "[1] \"f5605f62-72c4-4a13-8e03-3d2cd9b27be9.mupexi\"\n",
      "[1] \"f629617d-b9c6-4744-a131-f10ac27a6290.mupexi\"\n",
      "[1] \"f6d7d484-1bdc-4087-b04c-c3d7efb1b9ff.mupexi\"\n",
      "[1] \"f6e2ea5a-0970-4e02-b11e-d83180dddf55.mupexi\"\n",
      "[1] \"f73f0290-c5d9-4f3b-af96-4d6478ee56fd.mupexi\"\n",
      "[1] \"f7821ac2-7d58-4000-b269-01ee0af25270.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"f7aeb423-6763-499f-8c17-b956794c3dc9.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"f7b19fc4-1023-4f03-9761-6c8f2ce024ca.mupexi\"\n",
      "[1] \"f7c7afb5-7eab-4fda-a24f-57483e8dff34.mupexi\"\n",
      "[1] \"f801b048-6e87-4fa1-8cc8-45fce51a9865.mupexi\"\n",
      "[1] \"f810d954-c010-4bc4-b6cb-74b5f59fe7c0.mupexi\"\n",
      "[1] \"f8572aa5-cab7-4218-97cd-13b25b47eef6.mupexi\"\n",
      "[1] \"f9101293-57c8-448a-8ddc-8e2ad82d20ad.mupexi\"\n",
      "[1] \"fa6202c7-6328-41ad-b600-295f6405a829.mupexi\"\n"
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    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"fabbd7a6-53e4-4ff2-89a2-e036fe389f25.mupexi\"\n",
      "[1] \"fb38060f-5563-4b25-b3b5-f4ac807fd35f.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"fb766377-1d27-4d1f-8692-45b887a51427.mupexi\"\n",
      "[1] \"fc56202a-df9f-4e57-af3e-108a56808e30.mupexi\"\n",
      "[1] \"fc9ef947-ac81-4741-bd93-dee0e3dc76f5.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"fcb6fbf5-6045-4076-97c5-67f5027a44ca.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"fd982d34-29d2-450b-a9f5-541b8c7811a6.mupexi\"\n",
      "[1] \"fdf01de6-dba8-4ef8-b7b5-76ee8e53a00d.mupexi\"\n",
      "[1] \"ff436ec0-492c-414a-8564-74adaf4c9fac.mupexi\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "sample_id not found\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"ffdd6cc0-0b9f-488b-b5d0-6ed5908e98ea.mupexi\"\n"
     ]
    }
   ],
   "source": [
    "for(f in flelist){\n",
    "    print(f)\n",
    "    #get the filename\n",
    "    myfilename <- gsub(\".mupexi\", \"\", f)\n",
    "    #get sample_id by grepping filename from manifest file\n",
    "    mysample_id <- opti_mutect2_cbttc$sample_id[grepl(myfilename, opti_mutect2_cbttc$name)]\n",
    "    #skip if sample_id is not in CBTTC_data_maf\n",
    "    if(sum(CBTTC_data_maf$sample_id == mysample_id) == 0){ \n",
    "        message(\"sample_id not found\")\n",
    "        next}\n",
    "    # get overlapped vars for the sample_id\n",
    "    myoverlappedmutations <- CBTTC_data_maf[CBTTC_data_maf$sample_id == mysample_id,]\n",
    "    \n",
    "    #read the mupexi file\n",
    "    mymupexi <- read.table(file = paste0(mountpath, f),\n",
    "                        sep = \"\\t\", check.names = F, comment.char = \"#\",\n",
    "                        header = TRUE, stringsAsFactors = FALSE)\n",
    "    #skip if genes in mupexi output arent in overlapped mutations\n",
    "    if(sum(mymupexi$Gene_ID %in% myoverlappedmutations$Gene) == 0){ \n",
    "        message(\"Genes in mupexi not found in overlapped variants\")\n",
    "        next}\n",
    "    #subset to overlapped vars only using Ensembl IDs\n",
    "    mupexi_genes <- mymupexi[ mymupexi$Gene_ID %in% myoverlappedmutations$Gene,]\n",
    "    mupexi_genes_AA <- mupexi_genes[ mupexi_genes$Amino_Acid_Change %in% myoverlappedmutations$Amino_acids,]\n",
    "    # annotate binders for Norm and Mut\n",
    "    mupexi_genes_AA$Norm_MHCbinder <- NA\n",
    "    mupexi_genes_AA$Norm_MHCbinder[mupexi_genes_AA$Norm_MHCrank_BA <= 0.5] <- \"SB\"\n",
    "    mupexi_genes_AA$Norm_MHCbinder[mupexi_genes_AA$Norm_MHCrank_BA > 0.5 &\n",
    "                                   mupexi_genes_AA$Norm_MHCrank_BA <= 2] <- \"WB\"\n",
    "\n",
    "\n",
    "    mupexi_genes_AA$Mut_MHCbinder <- NA\n",
    "    mupexi_genes_AA$Mut_MHCbinder[mupexi_genes_AA$Mut_MHCrank_BA <= 0.5] <- \"SB\"\n",
    "    mupexi_genes_AA$Mut_MHCbinder[mupexi_genes_AA$Mut_MHCrank_BA > 0.5 &\n",
    "                                  mupexi_genes_AA$Mut_MHCrank_BA <= 2] <- \"WB\"\n",
    "    \n",
    "      \n",
    "    #Include all peptides\n",
    "    mupexi_genes_AA_binders <- mupexi_genes_AA #[ !is.na(mupexi_genes_AA$Mut_MHCbinder),]\n",
    "    \n",
    "    #skip if no SB or WB in mupexi output arent in overlapped mutations\n",
    "    if(nrow(mupexi_genes_AA_binders) == 0){ \n",
    "        message(\"No SB or WB found in Mut_MHC\")\n",
    "        next} \n",
    "    # add sample_id as variable\n",
    "    mupexi_genes_AA_binders$sample_id <- mysample_id\n",
    "    write.table(mupexi_genes_AA_binders,\n",
    "           file = paste0(datapath, \"Mupexi/\", mysample_id, \"_overlappedvar_all.mupexi\"), sep = \"\\t\", quote = F, row.names = F)\n",
    "    \n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## TARGET"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "mymaf_gdc <- read.maf(maf =  paste0(datapath, \"snv/GDC_allmaf_3VAF_fl_dedup_sampleid_KB.maf\"),\n",
    "                      useAll = TRUE, verbose = FALSE,\n",
    "                      vc_nonSyn = c(\"Frame_Shift_Del\", \"Frame_Shift_Ins\", \n",
    "                                    \"Nonsense_Mutation\",\"Nonstop_Mutation\", \n",
    "                                    \"In_Frame_Del\",\"In_Frame_Ins\", \n",
    "                                    \"Missense_Mutation\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "mymaf_gdc_data<- mymaf_gdc@data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "mymaf_gdc_data$Tumor_Sample_Barcode <- as.character(mymaf_gdc_data$Tumor_Sample_Barcode)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Subset to TARGET only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "mymaf_target_data <- mymaf_gdc_data[grepl(\"TARGET\", mymaf_gdc_data$Tumor_Sample_Barcode),]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "subset to samples included in total_mut_manifest_estimate_quanti"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "mymaf_target_data <- mymaf_target_data[mymaf_target_data$Tumor_Sample_Barcode %in% \n",
    "                                       total_mut_manifest_estimate$sample_id,]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "colnames(mymaf_target_data)[colnames(mymaf_target_data) == \"Tumor_Sample_Barcode\"] <- \"sample_id\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "98"
      ],
      "text/latex": [
       "98"
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      "text/markdown": [
       "98"
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      "text/plain": [
       "[1] 98"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(unique(mymaf_target_data$sample_id))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "read in optitype-mutect2 manifest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "opti_mutect2_target <- read.table(file = paste0(manifestpath, \"mutect2_optitype_manifest_target.txt\"),\n",
    "                        sep = \"\\t\", check.names = F, \n",
    "                        header = TRUE, stringsAsFactors = FALSE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "for(f in flelist){\n",
    "    print(f)\n",
    "    #get the filename\n",
    "    myfilename <- gsub(\".mupexi\", \"\", f)\n",
    "    #get sample_id by grepping filename from manifest file\n",
    "    mysample_id <- opti_mutect2_target$sample_id.x[grepl(myfilename, opti_mutect2_target$name.y)]\n",
    "    #skip if sample_id is not in CBTTC_data_maf\n",
    "    if(sum(mymaf_target_data$sample_id == mysample_id) == 0){ \n",
    "        message(\"sample_id not found\")\n",
    "        next}\n",
    "    # get overlapped vars for the sample_id\n",
    "    myoverlappedmutations <- mymaf_target_data[mymaf_target_data$sample_id == mysample_id,]\n",
    "    \n",
    "    #read the mupexi file\n",
    "    mymupexi <- read.table(file = paste0(mountpath, f),\n",
    "                        sep = \"\\t\", check.names = F, comment.char = \"#\",\n",
    "                        header = TRUE, stringsAsFactors = FALSE)\n",
    "    #skip if genes in mupexi output arent in overlapped mutations\n",
    "    if(sum(mymupexi$Gene_ID %in% myoverlappedmutations$Gene) == 0){ \n",
    "        message(\"Genes in mupexi not found in overlapped variants\")\n",
    "        next}\n",
    "    #subset to overlapped vars only using Ensembl IDs\n",
    "    mupexi_genes <- mymupexi[ mymupexi$Gene_ID %in% myoverlappedmutations$Gene,]\n",
    "    mupexi_genes_AA <- mupexi_genes[ mupexi_genes$Amino_Acid_Change %in% myoverlappedmutations$Amino_acids,]\n",
    "    # annotate binders for Norm and Mut\n",
    "    mupexi_genes_AA$Norm_MHCbinder <- NA\n",
    "    mupexi_genes_AA$Norm_MHCbinder[mupexi_genes_AA$Norm_MHCrank_BA <= 0.5] <- \"SB\"\n",
    "    mupexi_genes_AA$Norm_MHCbinder[mupexi_genes_AA$Norm_MHCrank_BA > 0.5 &\n",
    "                                   mupexi_genes_AA$Norm_MHCrank_BA <= 2] <- \"WB\"\n",
    "\n",
    "\n",
    "    mupexi_genes_AA$Mut_MHCbinder <- NA\n",
    "    mupexi_genes_AA$Mut_MHCbinder[mupexi_genes_AA$Mut_MHCrank_BA <= 0.5] <- \"SB\"\n",
    "    mupexi_genes_AA$Mut_MHCbinder[mupexi_genes_AA$Mut_MHCrank_BA > 0.5 &\n",
    "                                  mupexi_genes_AA$Mut_MHCrank_BA <= 2] <- \"WB\"\n",
    "    \n",
    "    #Include only those that Mut_MHCbinder is eather WB or SB\n",
    "    mupexi_genes_AA_binders <- mupexi_genes_AA#[ !is.na(mupexi_genes_AA$Mut_MHCbinder),]\n",
    "    #skip if no SB or WB in mupexi output arent in overlapped mutations\n",
    "    if(nrow(mupexi_genes_AA_binders) == 0){ \n",
    "        message(\"No SB or WB found in Mut_MHC\")\n",
    "        next} \n",
    "    # add sample_id as variable\n",
    "    mupexi_genes_AA_binders$sample_id <- mysample_id    \n",
    "    write.table(mupexi_genes_AA_binders,\n",
    "           file = paste0(datapath, \"Mupexi/\", mysample_id, \"_overlappedvar_all.mupexi\"), sep = \"\\t\", quote = F, row.names = F)\n",
    "    \n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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}