├── LICENSE
└── 1001genomes_PAM_GPN_correlation.ipynb


/LICENSE:
--------------------------------------------------------------------------------
 1 | MIT License
 2 | 
 3 | Copyright (c) 2025 Silvan Büdenbender
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 | 


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/1001genomes_PAM_GPN_correlation.ipynb:
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   1 | {
   2 |   "nbformat": 4,
   3 |   "nbformat_minor": 0,
   4 |   "metadata": {
   5 |     "colab": {
   6 |       "provenance": [],
   7 |       "authorship_tag": "ABX9TyNPlEba2v8XoRYdbXK+KCGE",
   8 |       "include_colab_link": true
   9 |     },
  10 |     "kernelspec": {
  11 |       "name": "python3",
  12 |       "display_name": "Python 3"
  13 |     },
  14 |     "language_info": {
  15 |       "name": "python"
  16 |     }
  17 |   },
  18 |   "cells": [
  19 |     {
  20 |       "cell_type": "markdown",
  21 |       "metadata": {
  22 |         "id": "view-in-github",
  23 |         "colab_type": "text"
  24 |       },
  25 |       "source": [
  26 |         "<a href=\"https://colab.research.google.com/github/SilvanCodes/ag_wiehe/blob/main/1001genomes_PAM_GPN_correlation.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
  27 |       ]
  28 |     },
  29 |     {
  30 |       "cell_type": "code",
  31 |       "source": [
  32 |         "!pip install biopython"
  33 |       ],
  34 |       "metadata": {
  35 |         "colab": {
  36 |           "base_uri": "https://localhost:8080/"
  37 |         },
  38 |         "id": "AcjQYlyybMKq",
  39 |         "outputId": "bbd6f38e-43af-44d2-a315-da76ad3f8241"
  40 |       },
  41 |       "execution_count": null,
  42 |       "outputs": [
  43 |         {
  44 |           "output_type": "stream",
  45 |           "name": "stdout",
  46 |           "text": [
  47 |             "Collecting biopython\n",
  48 |             "  Downloading biopython-1.86-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)\n",
  49 |             "Requirement already satisfied: numpy in /usr/local/lib/python3.12/dist-packages (from biopython) (2.0.2)\n",
  50 |             "Downloading biopython-1.86-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.2 MB)\n",
  51 |             "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.2/3.2 MB\u001b[0m \u001b[31m36.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
  52 |             "\u001b[?25hInstalling collected packages: biopython\n",
  53 |             "Successfully installed biopython-1.86\n"
  54 |           ]
  55 |         }
  56 |       ]
  57 |     },
  58 |     {
  59 |       "cell_type": "code",
  60 |       "source": [
  61 |         "import time\n",
  62 |         "import requests\n",
  63 |         "from collections import defaultdict\n",
  64 |         "from io import StringIO\n",
  65 |         "\n",
  66 |         "from tqdm import tqdm\n",
  67 |         "import pandas as pd\n",
  68 |         "import numpy as np\n",
  69 |         "from Bio import SeqIO\n",
  70 |         "from Bio.Seq import Seq, MutableSeq"
  71 |       ],
  72 |       "metadata": {
  73 |         "id": "k5L396sZ0qxA"
  74 |       },
  75 |       "execution_count": null,
  76 |       "outputs": []
  77 |     },
  78 |     {
  79 |       "cell_type": "code",
  80 |       "execution_count": null,
  81 |       "metadata": {
  82 |         "id": "hu4QRbwAzV7y"
  83 |       },
  84 |       "outputs": [],
  85 |       "source": [
  86 |         "HMA4_gene_id = \"AT2G19110.1\"\n",
  87 |         "amino_acid_substitution = \"missense_variant\""
  88 |       ]
  89 |     },
  90 |     {
  91 |       "cell_type": "code",
  92 |       "source": [
  93 |         "class DefaultDict(defaultdict):\n",
  94 |         "    def __missing__(self, key):\n",
  95 |         "        return self.default_factory(key)\n",
  96 |         "\n",
  97 |         "def get_accession_gene_fasta(gene):\n",
  98 |         "  def get_gene(accession):\n",
  99 |         "    fasta = requests.get(f\"https://tools.1001genomes.org/api/v1/pseudogenomes/strains/{accession}/gids/{gene}\")\n",
 100 |         "    return fasta.text\n",
 101 |         "  return get_gene\n"
 102 |       ],
 103 |       "metadata": {
 104 |         "id": "XozcmWeH5LBT"
 105 |       },
 106 |       "execution_count": null,
 107 |       "outputs": []
 108 |     },
 109 |     {
 110 |       "cell_type": "code",
 111 |       "source": [
 112 |         "HMA4_fasta_cache = DefaultDict(get_accession_gene_fasta(HMA4_gene_id))"
 113 |       ],
 114 |       "metadata": {
 115 |         "id": "KqQTiutV2Y0e"
 116 |       },
 117 |       "execution_count": null,
 118 |       "outputs": []
 119 |     },
 120 |     {
 121 |       "cell_type": "code",
 122 |       "source": [
 123 |         "aa_sub_snps = requests.get(f\"https://tools.1001genomes.org/api/v1.1/variants.json?type=snps;accs=all;gid={HMA4_gene_id};effect={amino_acid_substitution}\")\n",
 124 |         "df = pd.DataFrame(aa_sub_snps.json()['data'], columns=[\"chromosome\", \"position\", \"accession\", \"reference\", \"variant\", \"-\", \"impacts\", \"effects\"])\n",
 125 |         "df"
 126 |       ],
 127 |       "metadata": {
 128 |         "id": "S25ZOM6u0zBX",
 129 |         "colab": {
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 132 |         },
 133 |         "outputId": "d54e94fd-560b-4097-e523-63bb4556b389"
 134 |       },
 135 |       "execution_count": null,
 136 |       "outputs": [
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 141 |               "      chromosome  position  accession reference variant   -   impacts  \\\n",
 142 |               "0              2   8279523       9653         T       G  40  MODERATE   \n",
 143 |               "1              2   8279523       9655         T       G  40  MODERATE   \n",
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 151 |               "2331           2   8286155       9894         G       T  40  MODERATE   \n",
 152 |               "2332           2   8286250       9121         G       A  40  MODERATE   \n",
 153 |               "\n",
 154 |               "               effects  \n",
 155 |               "0     missense_variant  \n",
 156 |               "1     missense_variant  \n",
 157 |               "2     missense_variant  \n",
 158 |               "3     missense_variant  \n",
 159 |               "4     missense_variant  \n",
 160 |               "...                ...  \n",
 161 |               "2328  missense_variant  \n",
 162 |               "2329  missense_variant  \n",
 163 |               "2330  missense_variant  \n",
 164 |               "2331  missense_variant  \n",
 165 |               "2332  missense_variant  \n",
 166 |               "\n",
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 455 |               "\n",
 456 |               "  .colab-df-quickchart-complete:disabled,\n",
 457 |               "  .colab-df-quickchart-complete:disabled:hover {\n",
 458 |               "    background-color: var(--disabled-bg-color);\n",
 459 |               "    fill: var(--disabled-fill-color);\n",
 460 |               "    box-shadow: none;\n",
 461 |               "  }\n",
 462 |               "\n",
 463 |               "  .colab-df-spinner {\n",
 464 |               "    border: 2px solid var(--fill-color);\n",
 465 |               "    border-color: transparent;\n",
 466 |               "    border-bottom-color: var(--fill-color);\n",
 467 |               "    animation:\n",
 468 |               "      spin 1s steps(1) infinite;\n",
 469 |               "  }\n",
 470 |               "\n",
 471 |               "  @keyframes spin {\n",
 472 |               "    0% {\n",
 473 |               "      border-color: transparent;\n",
 474 |               "      border-bottom-color: var(--fill-color);\n",
 475 |               "      border-left-color: var(--fill-color);\n",
 476 |               "    }\n",
 477 |               "    20% {\n",
 478 |               "      border-color: transparent;\n",
 479 |               "      border-left-color: var(--fill-color);\n",
 480 |               "      border-top-color: var(--fill-color);\n",
 481 |               "    }\n",
 482 |               "    30% {\n",
 483 |               "      border-color: transparent;\n",
 484 |               "      border-left-color: var(--fill-color);\n",
 485 |               "      border-top-color: var(--fill-color);\n",
 486 |               "      border-right-color: var(--fill-color);\n",
 487 |               "    }\n",
 488 |               "    40% {\n",
 489 |               "      border-color: transparent;\n",
 490 |               "      border-right-color: var(--fill-color);\n",
 491 |               "      border-top-color: var(--fill-color);\n",
 492 |               "    }\n",
 493 |               "    60% {\n",
 494 |               "      border-color: transparent;\n",
 495 |               "      border-right-color: var(--fill-color);\n",
 496 |               "    }\n",
 497 |               "    80% {\n",
 498 |               "      border-color: transparent;\n",
 499 |               "      border-right-color: var(--fill-color);\n",
 500 |               "      border-bottom-color: var(--fill-color);\n",
 501 |               "    }\n",
 502 |               "    90% {\n",
 503 |               "      border-color: transparent;\n",
 504 |               "      border-bottom-color: var(--fill-color);\n",
 505 |               "    }\n",
 506 |               "  }\n",
 507 |               "</style>\n",
 508 |               "\n",
 509 |               "      <script>\n",
 510 |               "        async function quickchart(key) {\n",
 511 |               "          const quickchartButtonEl =\n",
 512 |               "            document.querySelector('#' + key + ' button');\n",
 513 |               "          quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
 514 |               "          quickchartButtonEl.classList.add('colab-df-spinner');\n",
 515 |               "          try {\n",
 516 |               "            const charts = await google.colab.kernel.invokeFunction(\n",
 517 |               "                'suggestCharts', [key], {});\n",
 518 |               "          } catch (error) {\n",
 519 |               "            console.error('Error during call to suggestCharts:', error);\n",
 520 |               "          }\n",
 521 |               "          quickchartButtonEl.classList.remove('colab-df-spinner');\n",
 522 |               "          quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
 523 |               "        }\n",
 524 |               "        (() => {\n",
 525 |               "          let quickchartButtonEl =\n",
 526 |               "            document.querySelector('#df-a52d84eb-6c9e-4f87-8a11-acc432315ad8 button');\n",
 527 |               "          quickchartButtonEl.style.display =\n",
 528 |               "            google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
 529 |               "        })();\n",
 530 |               "      </script>\n",
 531 |               "    </div>\n",
 532 |               "\n",
 533 |               "  <div id=\"id_db309731-c0c5-44dd-801e-ecf396d179d1\">\n",
 534 |               "    <style>\n",
 535 |               "      .colab-df-generate {\n",
 536 |               "        background-color: #E8F0FE;\n",
 537 |               "        border: none;\n",
 538 |               "        border-radius: 50%;\n",
 539 |               "        cursor: pointer;\n",
 540 |               "        display: none;\n",
 541 |               "        fill: #1967D2;\n",
 542 |               "        height: 32px;\n",
 543 |               "        padding: 0 0 0 0;\n",
 544 |               "        width: 32px;\n",
 545 |               "      }\n",
 546 |               "\n",
 547 |               "      .colab-df-generate:hover {\n",
 548 |               "        background-color: #E2EBFA;\n",
 549 |               "        box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
 550 |               "        fill: #174EA6;\n",
 551 |               "      }\n",
 552 |               "\n",
 553 |               "      [theme=dark] .colab-df-generate {\n",
 554 |               "        background-color: #3B4455;\n",
 555 |               "        fill: #D2E3FC;\n",
 556 |               "      }\n",
 557 |               "\n",
 558 |               "      [theme=dark] .colab-df-generate:hover {\n",
 559 |               "        background-color: #434B5C;\n",
 560 |               "        box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
 561 |               "        filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
 562 |               "        fill: #FFFFFF;\n",
 563 |               "      }\n",
 564 |               "    </style>\n",
 565 |               "    <button class=\"colab-df-generate\" onclick=\"generateWithVariable('df')\"\n",
 566 |               "            title=\"Generate code using this dataframe.\"\n",
 567 |               "            style=\"display:none;\">\n",
 568 |               "\n",
 569 |               "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
 570 |               "       width=\"24px\">\n",
 571 |               "    <path d=\"M7,19H8.4L18.45,9,17,7.55,7,17.6ZM5,21V16.75L18.45,3.32a2,2,0,0,1,2.83,0l1.4,1.43a1.91,1.91,0,0,1,.58,1.4,1.91,1.91,0,0,1-.58,1.4L9.25,21ZM18.45,9,17,7.55Zm-12,3A5.31,5.31,0,0,0,4.9,8.1,5.31,5.31,0,0,0,1,6.5,5.31,5.31,0,0,0,4.9,4.9,5.31,5.31,0,0,0,6.5,1,5.31,5.31,0,0,0,8.1,4.9,5.31,5.31,0,0,0,12,6.5,5.46,5.46,0,0,0,6.5,12Z\"/>\n",
 572 |               "  </svg>\n",
 573 |               "    </button>\n",
 574 |               "    <script>\n",
 575 |               "      (() => {\n",
 576 |               "      const buttonEl =\n",
 577 |               "        document.querySelector('#id_db309731-c0c5-44dd-801e-ecf396d179d1 button.colab-df-generate');\n",
 578 |               "      buttonEl.style.display =\n",
 579 |               "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
 580 |               "\n",
 581 |               "      buttonEl.onclick = () => {\n",
 582 |               "        google.colab.notebook.generateWithVariable('df');\n",
 583 |               "      }\n",
 584 |               "      })();\n",
 585 |               "    </script>\n",
 586 |               "  </div>\n",
 587 |               "\n",
 588 |               "    </div>\n",
 589 |               "  </div>\n"
 590 |             ],
 591 |             "application/vnd.google.colaboratory.intrinsic+json": {
 592 |               "type": "dataframe",
 593 |               "variable_name": "df",
 594 |               "summary": "{\n  \"name\": \"df\",\n  \"rows\": 2333,\n  \"fields\": [\n    {\n      \"column\": \"chromosome\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 0,\n        \"min\": 2,\n        \"max\": 2,\n        \"num_unique_values\": 1,\n        \"samples\": [\n          2\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"position\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 1083,\n        \"min\": 8279523,\n        \"max\": 8286250,\n        \"num_unique_values\": 83,\n        \"samples\": [\n          8284492\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"accession\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 2602,\n        \"min\": 88,\n        \"max\": 18696,\n        \"num_unique_values\": 959,\n        \"samples\": [\n          10010\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"reference\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 4,\n        \"samples\": [\n          \"G\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"variant\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 4,\n        \"samples\": [\n          \"A\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"-\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 0,\n        \"min\": 40,\n        \"max\": 40,\n        \"num_unique_values\": 1,\n        \"samples\": [\n          40\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"impacts\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"MODERATE\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"effects\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"missense_variant\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
 595 |             }
 596 |           },
 597 |           "metadata": {},
 598 |           "execution_count": 122
 599 |         }
 600 |       ]
 601 |     },
 602 |     {
 603 |       "cell_type": "code",
 604 |       "source": [
 605 |         "def get_start_end_from_seq(seq):\n",
 606 |         "  range = seq.id.split(\"|\")[4]\n",
 607 |         "  _chrom, range = range.split(\":\")\n",
 608 |         "  start, end = range.split(\"..\")\n",
 609 |         "  return int(start), int(end)"
 610 |       ],
 611 |       "metadata": {
 612 |         "id": "MCg0jtLcgNWn"
 613 |       },
 614 |       "execution_count": null,
 615 |       "outputs": []
 616 |     },
 617 |     {
 618 |       "cell_type": "code",
 619 |       "source": [
 620 |         "def get_aa_substitution_pair(variant, record, in_gene_position):\n",
 621 |         "  in_condon_position = in_gene_position % 3\n",
 622 |         "\n",
 623 |         "  codon_start = (in_gene_position // 3) * 3\n",
 624 |         "  codon = MutableSeq(record.seq[codon_start:codon_start+3])\n",
 625 |         "\n",
 626 |         "  variant_aa = codon.translate()\n",
 627 |         "\n",
 628 |         "  codon[in_condon_position] = variant[\"reference\"]\n",
 629 |         "  reference_aa = codon.translate()\n",
 630 |         "\n",
 631 |         "  return reference_aa, variant_aa"
 632 |       ],
 633 |       "metadata": {
 634 |         "id": "4lrKW5Fkkf7J"
 635 |       },
 636 |       "execution_count": null,
 637 |       "outputs": []
 638 |     },
 639 |     {
 640 |       "cell_type": "code",
 641 |       "source": [
 642 |         "def build_variant_substitution_data(variant, fasta_cache):\n",
 643 |         "  fasta = fasta_cache[variant[\"accession\"]]\n",
 644 |         "  record = SeqIO.read(StringIO(fasta), \"fasta\")\n",
 645 |         "\n",
 646 |         "  start, _ = get_start_end_from_seq(record)\n",
 647 |         "  in_gene_position = variant[\"position\"] - start\n",
 648 |         "\n",
 649 |         "  if variant[\"variant\"] == record.seq[in_gene_position]:\n",
 650 |         "\n",
 651 |         "    snp_centered_dna_window = record.seq[in_gene_position-256:in_gene_position+257]\n",
 652 |         "\n",
 653 |         "    reference_aa, variant_aa = get_aa_substitution_pair(variant, record, in_gene_position)\n",
 654 |         "\n",
 655 |         "    return [str(reference_aa), str(variant_aa), str(snp_centered_dna_window)]\n",
 656 |         "  else:\n",
 657 |         "    return [\"-\", \"-\", \"-\"]"
 658 |       ],
 659 |       "metadata": {
 660 |         "id": "xD7FLy-Ioi2o"
 661 |       },
 662 |       "execution_count": null,
 663 |       "outputs": []
 664 |     },
 665 |     {
 666 |       "cell_type": "code",
 667 |       "source": [
 668 |         "df[:2]"
 669 |       ],
 670 |       "metadata": {
 671 |         "colab": {
 672 |           "base_uri": "https://localhost:8080/",
 673 |           "height": 112
 674 |         },
 675 |         "id": "yKJXVDJFr-Z4",
 676 |         "outputId": "fb20756f-3684-491d-cfe8-36bd2fba62b1"
 677 |       },
 678 |       "execution_count": null,
 679 |       "outputs": [
 680 |         {
 681 |           "output_type": "execute_result",
 682 |           "data": {
 683 |             "text/plain": [
 684 |               "   chromosome  position  accession reference variant   -   impacts  \\\n",
 685 |               "0           2   8279523       9653         T       G  40  MODERATE   \n",
 686 |               "1           2   8279523       9655         T       G  40  MODERATE   \n",
 687 |               "\n",
 688 |               "            effects  \n",
 689 |               "0  missense_variant  \n",
 690 |               "1  missense_variant  "
 691 |             ],
 692 |             "text/html": [
 693 |               "\n",
 694 |               "  <div id=\"df-b4b64bdb-1f86-4cd2-b984-0886aec740b3\" class=\"colab-df-container\">\n",
 695 |               "    <div>\n",
 696 |               "<style scoped>\n",
 697 |               "    .dataframe tbody tr th:only-of-type {\n",
 698 |               "        vertical-align: middle;\n",
 699 |               "    }\n",
 700 |               "\n",
 701 |               "    .dataframe tbody tr th {\n",
 702 |               "        vertical-align: top;\n",
 703 |               "    }\n",
 704 |               "\n",
 705 |               "    .dataframe thead th {\n",
 706 |               "        text-align: right;\n",
 707 |               "    }\n",
 708 |               "</style>\n",
 709 |               "<table border=\"1\" class=\"dataframe\">\n",
 710 |               "  <thead>\n",
 711 |               "    <tr style=\"text-align: right;\">\n",
 712 |               "      <th></th>\n",
 713 |               "      <th>chromosome</th>\n",
 714 |               "      <th>position</th>\n",
 715 |               "      <th>accession</th>\n",
 716 |               "      <th>reference</th>\n",
 717 |               "      <th>variant</th>\n",
 718 |               "      <th>-</th>\n",
 719 |               "      <th>impacts</th>\n",
 720 |               "      <th>effects</th>\n",
 721 |               "    </tr>\n",
 722 |               "  </thead>\n",
 723 |               "  <tbody>\n",
 724 |               "    <tr>\n",
 725 |               "      <th>0</th>\n",
 726 |               "      <td>2</td>\n",
 727 |               "      <td>8279523</td>\n",
 728 |               "      <td>9653</td>\n",
 729 |               "      <td>T</td>\n",
 730 |               "      <td>G</td>\n",
 731 |               "      <td>40</td>\n",
 732 |               "      <td>MODERATE</td>\n",
 733 |               "      <td>missense_variant</td>\n",
 734 |               "    </tr>\n",
 735 |               "    <tr>\n",
 736 |               "      <th>1</th>\n",
 737 |               "      <td>2</td>\n",
 738 |               "      <td>8279523</td>\n",
 739 |               "      <td>9655</td>\n",
 740 |               "      <td>T</td>\n",
 741 |               "      <td>G</td>\n",
 742 |               "      <td>40</td>\n",
 743 |               "      <td>MODERATE</td>\n",
 744 |               "      <td>missense_variant</td>\n",
 745 |               "    </tr>\n",
 746 |               "  </tbody>\n",
 747 |               "</table>\n",
 748 |               "</div>\n",
 749 |               "    <div class=\"colab-df-buttons\">\n",
 750 |               "\n",
 751 |               "  <div class=\"colab-df-container\">\n",
 752 |               "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-b4b64bdb-1f86-4cd2-b984-0886aec740b3')\"\n",
 753 |               "            title=\"Convert this dataframe to an interactive table.\"\n",
 754 |               "            style=\"display:none;\">\n",
 755 |               "\n",
 756 |               "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
 757 |               "    <path d=\"M120-120v-720h720v720H120Zm60-500h600v-160H180v160Zm220 220h160v-160H400v160Zm0 220h160v-160H400v160ZM180-400h160v-160H180v160Zm440 0h160v-160H620v160ZM180-180h160v-160H180v160Zm440 0h160v-160H620v160Z\"/>\n",
 758 |               "  </svg>\n",
 759 |               "    </button>\n",
 760 |               "\n",
 761 |               "  <style>\n",
 762 |               "    .colab-df-container {\n",
 763 |               "      display:flex;\n",
 764 |               "      gap: 12px;\n",
 765 |               "    }\n",
 766 |               "\n",
 767 |               "    .colab-df-convert {\n",
 768 |               "      background-color: #E8F0FE;\n",
 769 |               "      border: none;\n",
 770 |               "      border-radius: 50%;\n",
 771 |               "      cursor: pointer;\n",
 772 |               "      display: none;\n",
 773 |               "      fill: #1967D2;\n",
 774 |               "      height: 32px;\n",
 775 |               "      padding: 0 0 0 0;\n",
 776 |               "      width: 32px;\n",
 777 |               "    }\n",
 778 |               "\n",
 779 |               "    .colab-df-convert:hover {\n",
 780 |               "      background-color: #E2EBFA;\n",
 781 |               "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
 782 |               "      fill: #174EA6;\n",
 783 |               "    }\n",
 784 |               "\n",
 785 |               "    .colab-df-buttons div {\n",
 786 |               "      margin-bottom: 4px;\n",
 787 |               "    }\n",
 788 |               "\n",
 789 |               "    [theme=dark] .colab-df-convert {\n",
 790 |               "      background-color: #3B4455;\n",
 791 |               "      fill: #D2E3FC;\n",
 792 |               "    }\n",
 793 |               "\n",
 794 |               "    [theme=dark] .colab-df-convert:hover {\n",
 795 |               "      background-color: #434B5C;\n",
 796 |               "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
 797 |               "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
 798 |               "      fill: #FFFFFF;\n",
 799 |               "    }\n",
 800 |               "  </style>\n",
 801 |               "\n",
 802 |               "    <script>\n",
 803 |               "      const buttonEl =\n",
 804 |               "        document.querySelector('#df-b4b64bdb-1f86-4cd2-b984-0886aec740b3 button.colab-df-convert');\n",
 805 |               "      buttonEl.style.display =\n",
 806 |               "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
 807 |               "\n",
 808 |               "      async function convertToInteractive(key) {\n",
 809 |               "        const element = document.querySelector('#df-b4b64bdb-1f86-4cd2-b984-0886aec740b3');\n",
 810 |               "        const dataTable =\n",
 811 |               "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
 812 |               "                                                    [key], {});\n",
 813 |               "        if (!dataTable) return;\n",
 814 |               "\n",
 815 |               "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
 816 |               "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
 817 |               "          + ' to learn more about interactive tables.';\n",
 818 |               "        element.innerHTML = '';\n",
 819 |               "        dataTable['output_type'] = 'display_data';\n",
 820 |               "        await google.colab.output.renderOutput(dataTable, element);\n",
 821 |               "        const docLink = document.createElement('div');\n",
 822 |               "        docLink.innerHTML = docLinkHtml;\n",
 823 |               "        element.appendChild(docLink);\n",
 824 |               "      }\n",
 825 |               "    </script>\n",
 826 |               "  </div>\n",
 827 |               "\n",
 828 |               "\n",
 829 |               "    <div id=\"df-bc8eeb94-5829-4353-9c59-38e196842961\">\n",
 830 |               "      <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-bc8eeb94-5829-4353-9c59-38e196842961')\"\n",
 831 |               "                title=\"Suggest charts\"\n",
 832 |               "                style=\"display:none;\">\n",
 833 |               "\n",
 834 |               "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
 835 |               "     width=\"24px\">\n",
 836 |               "    <g>\n",
 837 |               "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
 838 |               "    </g>\n",
 839 |               "</svg>\n",
 840 |               "      </button>\n",
 841 |               "\n",
 842 |               "<style>\n",
 843 |               "  .colab-df-quickchart {\n",
 844 |               "      --bg-color: #E8F0FE;\n",
 845 |               "      --fill-color: #1967D2;\n",
 846 |               "      --hover-bg-color: #E2EBFA;\n",
 847 |               "      --hover-fill-color: #174EA6;\n",
 848 |               "      --disabled-fill-color: #AAA;\n",
 849 |               "      --disabled-bg-color: #DDD;\n",
 850 |               "  }\n",
 851 |               "\n",
 852 |               "  [theme=dark] .colab-df-quickchart {\n",
 853 |               "      --bg-color: #3B4455;\n",
 854 |               "      --fill-color: #D2E3FC;\n",
 855 |               "      --hover-bg-color: #434B5C;\n",
 856 |               "      --hover-fill-color: #FFFFFF;\n",
 857 |               "      --disabled-bg-color: #3B4455;\n",
 858 |               "      --disabled-fill-color: #666;\n",
 859 |               "  }\n",
 860 |               "\n",
 861 |               "  .colab-df-quickchart {\n",
 862 |               "    background-color: var(--bg-color);\n",
 863 |               "    border: none;\n",
 864 |               "    border-radius: 50%;\n",
 865 |               "    cursor: pointer;\n",
 866 |               "    display: none;\n",
 867 |               "    fill: var(--fill-color);\n",
 868 |               "    height: 32px;\n",
 869 |               "    padding: 0;\n",
 870 |               "    width: 32px;\n",
 871 |               "  }\n",
 872 |               "\n",
 873 |               "  .colab-df-quickchart:hover {\n",
 874 |               "    background-color: var(--hover-bg-color);\n",
 875 |               "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
 876 |               "    fill: var(--button-hover-fill-color);\n",
 877 |               "  }\n",
 878 |               "\n",
 879 |               "  .colab-df-quickchart-complete:disabled,\n",
 880 |               "  .colab-df-quickchart-complete:disabled:hover {\n",
 881 |               "    background-color: var(--disabled-bg-color);\n",
 882 |               "    fill: var(--disabled-fill-color);\n",
 883 |               "    box-shadow: none;\n",
 884 |               "  }\n",
 885 |               "\n",
 886 |               "  .colab-df-spinner {\n",
 887 |               "    border: 2px solid var(--fill-color);\n",
 888 |               "    border-color: transparent;\n",
 889 |               "    border-bottom-color: var(--fill-color);\n",
 890 |               "    animation:\n",
 891 |               "      spin 1s steps(1) infinite;\n",
 892 |               "  }\n",
 893 |               "\n",
 894 |               "  @keyframes spin {\n",
 895 |               "    0% {\n",
 896 |               "      border-color: transparent;\n",
 897 |               "      border-bottom-color: var(--fill-color);\n",
 898 |               "      border-left-color: var(--fill-color);\n",
 899 |               "    }\n",
 900 |               "    20% {\n",
 901 |               "      border-color: transparent;\n",
 902 |               "      border-left-color: var(--fill-color);\n",
 903 |               "      border-top-color: var(--fill-color);\n",
 904 |               "    }\n",
 905 |               "    30% {\n",
 906 |               "      border-color: transparent;\n",
 907 |               "      border-left-color: var(--fill-color);\n",
 908 |               "      border-top-color: var(--fill-color);\n",
 909 |               "      border-right-color: var(--fill-color);\n",
 910 |               "    }\n",
 911 |               "    40% {\n",
 912 |               "      border-color: transparent;\n",
 913 |               "      border-right-color: var(--fill-color);\n",
 914 |               "      border-top-color: var(--fill-color);\n",
 915 |               "    }\n",
 916 |               "    60% {\n",
 917 |               "      border-color: transparent;\n",
 918 |               "      border-right-color: var(--fill-color);\n",
 919 |               "    }\n",
 920 |               "    80% {\n",
 921 |               "      border-color: transparent;\n",
 922 |               "      border-right-color: var(--fill-color);\n",
 923 |               "      border-bottom-color: var(--fill-color);\n",
 924 |               "    }\n",
 925 |               "    90% {\n",
 926 |               "      border-color: transparent;\n",
 927 |               "      border-bottom-color: var(--fill-color);\n",
 928 |               "    }\n",
 929 |               "  }\n",
 930 |               "</style>\n",
 931 |               "\n",
 932 |               "      <script>\n",
 933 |               "        async function quickchart(key) {\n",
 934 |               "          const quickchartButtonEl =\n",
 935 |               "            document.querySelector('#' + key + ' button');\n",
 936 |               "          quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
 937 |               "          quickchartButtonEl.classList.add('colab-df-spinner');\n",
 938 |               "          try {\n",
 939 |               "            const charts = await google.colab.kernel.invokeFunction(\n",
 940 |               "                'suggestCharts', [key], {});\n",
 941 |               "          } catch (error) {\n",
 942 |               "            console.error('Error during call to suggestCharts:', error);\n",
 943 |               "          }\n",
 944 |               "          quickchartButtonEl.classList.remove('colab-df-spinner');\n",
 945 |               "          quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
 946 |               "        }\n",
 947 |               "        (() => {\n",
 948 |               "          let quickchartButtonEl =\n",
 949 |               "            document.querySelector('#df-bc8eeb94-5829-4353-9c59-38e196842961 button');\n",
 950 |               "          quickchartButtonEl.style.display =\n",
 951 |               "            google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
 952 |               "        })();\n",
 953 |               "      </script>\n",
 954 |               "    </div>\n",
 955 |               "\n",
 956 |               "    </div>\n",
 957 |               "  </div>\n"
 958 |             ],
 959 |             "application/vnd.google.colaboratory.intrinsic+json": {
 960 |               "type": "dataframe",
 961 |               "summary": "{\n  \"name\": \"df[:2]\",\n  \"rows\": 2,\n  \"fields\": [\n    {\n      \"column\": \"chromosome\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 0,\n        \"min\": 2,\n        \"max\": 2,\n        \"num_unique_values\": 1,\n        \"samples\": [\n          2\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"position\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 0,\n        \"min\": 8279523,\n        \"max\": 8279523,\n        \"num_unique_values\": 1,\n        \"samples\": [\n          8279523\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"accession\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 1,\n        \"min\": 9653,\n        \"max\": 9655,\n        \"num_unique_values\": 2,\n        \"samples\": [\n          9655\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"reference\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"T\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"variant\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"G\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"-\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 0,\n        \"min\": 40,\n        \"max\": 40,\n        \"num_unique_values\": 1,\n        \"samples\": [\n          40\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"impacts\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"MODERATE\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"effects\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          \"missense_variant\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
 962 |             }
 963 |           },
 964 |           "metadata": {},
 965 |           "execution_count": 95
 966 |         }
 967 |       ]
 968 |     },
 969 |     {
 970 |       "cell_type": "code",
 971 |       "source": [
 972 |         "results = []\n",
 973 |         "for variant in tqdm(df[:100].to_dict(orient=\"records\")):\n",
 974 |         "    results.append(build_variant_substitution_data(variant, HMA4_fasta_cache))\n",
 975 |         "    time.sleep(0.51)"
 976 |       ],
 977 |       "metadata": {
 978 |         "colab": {
 979 |           "base_uri": "https://localhost:8080/"
 980 |         },
 981 |         "id": "6Eg_-mHurtL0",
 982 |         "outputId": "4935ecc6-65d9-4852-bc4f-f82c206fc9ee"
 983 |       },
 984 |       "execution_count": null,
 985 |       "outputs": [
 986 |         {
 987 |           "output_type": "stream",
 988 |           "name": "stderr",
 989 |           "text": [
 990 |             "100%|██████████| 100/100 [01:34<00:00,  1.05it/s]\n"
 991 |           ]
 992 |         }
 993 |       ]
 994 |     },
 995 |     {
 996 |       "cell_type": "code",
 997 |       "source": [
 998 |         "build_variant_substitution_data(df.iloc[29], HMA4_fasta_cache)"
 999 |       ],
1000 |       "metadata": {
1001 |         "colab": {
1002 |           "base_uri": "https://localhost:8080/",
1003 |           "height": 297
1004 |         },
1005 |         "id": "ZETYFRvMyO74",
1006 |         "outputId": "db46b392-25e1-4e52-d46d-74e5b77acecf"
1007 |       },
1008 |       "execution_count": null,
1009 |       "outputs": [
1010 |         {
1011 |           "output_type": "error",
1012 |           "ename": "AssertionError",
1013 |           "evalue": "",
1014 |           "traceback": [
1015 |             "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
1016 |             "\u001b[0;31mAssertionError\u001b[0m                            Traceback (most recent call last)",
1017 |             "\u001b[0;32m/tmp/ipython-input-3953702373.py\u001b[0m in \u001b[0;36m<cell line: 0>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mbuild_variant_substitution_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m29\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mHMA4_fasta_cache\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0miloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m29\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
1018 |             "\u001b[0;32m/tmp/ipython-input-3100140708.py\u001b[0m in \u001b[0;36mbuild_variant_substitution_data\u001b[0;34m(variant, fasta_cache)\u001b[0m\n\u001b[1;32m      5\u001b[0m   \u001b[0mstart\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_start_end_from_seq\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrecord\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m   \u001b[0min_gene_position\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvariant\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"position\"\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mstart\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 7\u001b[0;31m   \u001b[0;32massert\u001b[0m \u001b[0mvariant\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"variant\"\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mrecord\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mseq\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0min_gene_position\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      9\u001b[0m   \u001b[0msnp_centered_dna_window\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrecord\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mseq\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0min_gene_position\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m256\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0min_gene_position\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;36m257\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
1019 |             "\u001b[0;31mAssertionError\u001b[0m: "
1020 |           ]
1021 |         }
1022 |       ]
1023 |     },
1024 |     {
1025 |       "cell_type": "code",
1026 |       "source": [
1027 |         "weird_variant = df.iloc[29]\n",
1028 |         "\n",
1029 |         "fasta = HMA4_fasta_cache[weird_variant[\"accession\"]]\n",
1030 |         "record = SeqIO.read(StringIO(fasta), \"fasta\")\n",
1031 |         "\n",
1032 |         "start, _ = get_start_end_from_seq(record)\n",
1033 |         "in_gene_position = weird_variant[\"position\"] - start\n",
1034 |         "\n",
1035 |         "print(record.seq[in_gene_position])\n",
1036 |         "print(weird_variant)\n"
1037 |       ],
1038 |       "metadata": {
1039 |         "colab": {
1040 |           "base_uri": "https://localhost:8080/"
1041 |         },
1042 |         "id": "o-a68W2eygrL",
1043 |         "outputId": "8f4c6a75-6028-4574-d94f-aa06ae8234aa"
1044 |       },
1045 |       "execution_count": null,
1046 |       "outputs": [
1047 |         {
1048 |           "output_type": "stream",
1049 |           "name": "stdout",
1050 |           "text": [
1051 |             "G\n",
1052 |             "chromosome                   2\n",
1053 |             "position               8280931\n",
1054 |             "accession                 9511\n",
1055 |             "reference                    G\n",
1056 |             "variant                      T\n",
1057 |             "-                           40\n",
1058 |             "impacts               MODERATE\n",
1059 |             "effects       missense_variant\n",
1060 |             "Name: 29, dtype: object\n"
1061 |           ]
1062 |         }
1063 |       ]
1064 |     },
1065 |     {
1066 |       "cell_type": "code",
1067 |       "source": [
1068 |         "results = pd.DataFrame(results, columns=[\"reference_aa\", \"variant_aa\", \"snp_centered_dna_window\"])\n",
1069 |         "results"
1070 |       ],
1071 |       "metadata": {
1072 |         "colab": {
1073 |           "base_uri": "https://localhost:8080/",
1074 |           "height": 424
1075 |         },
1076 |         "id": "heS0L3zyuyin",
1077 |         "outputId": "d8dde231-0d38-42fa-8be3-ce1d9d66dedb"
1078 |       },
1079 |       "execution_count": null,
1080 |       "outputs": [
1081 |         {
1082 |           "output_type": "execute_result",
1083 |           "data": {
1084 |             "text/plain": [
1085 |               "   reference_aa variant_aa                            snp_centered_dna_window\n",
1086 |               "0             L          V  AAAAGTAAACATTTTCAATAAGAAAATACAAGACCCATACCGAAAG...\n",
1087 |               "1             L          V  AAAAGTAAACATTTTCAATAAGAAANNNNNNNNNNNNNNNNNNNNG...\n",
1088 |               "2             L          V  AAAAGTAAACATTTTCAATAAGAAAATACAAGACCCATACCGAAAG...\n",
1089 |               "3             L          V  NNAAGTAAANNNNTNNAATAANAAAATACAAGACCCATNCCGAAAG...\n",
1090 |               "4             F          Y  AATAAGAAAANNNNNNNNNNNNNNCGNAAGTTTNTTNNNNANAAAA...\n",
1091 |               "..          ...        ...                                                ...\n",
1092 |               "95            K          M  TATAACAATTGTGAAATCTCTTGCTATTTTTATAAATGATTTTGAA...\n",
1093 |               "96            Y          F  CAATTGTGAAATCTCTTGCTATTTTTATAAATGATTTTGAAGTTGA...\n",
1094 |               "97            -          -                                                  -\n",
1095 |               "98            -          -                                                  -\n",
1096 |               "99            -          -                                                  -\n",
1097 |               "\n",
1098 |               "[100 rows x 3 columns]"
1099 |             ],
1100 |             "text/html": [
1101 |               "\n",
1102 |               "  <div id=\"df-feee07ef-00cd-413a-b52d-f5afaa83663d\" class=\"colab-df-container\">\n",
1103 |               "    <div>\n",
1104 |               "<style scoped>\n",
1105 |               "    .dataframe tbody tr th:only-of-type {\n",
1106 |               "        vertical-align: middle;\n",
1107 |               "    }\n",
1108 |               "\n",
1109 |               "    .dataframe tbody tr th {\n",
1110 |               "        vertical-align: top;\n",
1111 |               "    }\n",
1112 |               "\n",
1113 |               "    .dataframe thead th {\n",
1114 |               "        text-align: right;\n",
1115 |               "    }\n",
1116 |               "</style>\n",
1117 |               "<table border=\"1\" class=\"dataframe\">\n",
1118 |               "  <thead>\n",
1119 |               "    <tr style=\"text-align: right;\">\n",
1120 |               "      <th></th>\n",
1121 |               "      <th>reference_aa</th>\n",
1122 |               "      <th>variant_aa</th>\n",
1123 |               "      <th>snp_centered_dna_window</th>\n",
1124 |               "    </tr>\n",
1125 |               "  </thead>\n",
1126 |               "  <tbody>\n",
1127 |               "    <tr>\n",
1128 |               "      <th>0</th>\n",
1129 |               "      <td>L</td>\n",
1130 |               "      <td>V</td>\n",
1131 |               "      <td>AAAAGTAAACATTTTCAATAAGAAAATACAAGACCCATACCGAAAG...</td>\n",
1132 |               "    </tr>\n",
1133 |               "    <tr>\n",
1134 |               "      <th>1</th>\n",
1135 |               "      <td>L</td>\n",
1136 |               "      <td>V</td>\n",
1137 |               "      <td>AAAAGTAAACATTTTCAATAAGAAANNNNNNNNNNNNNNNNNNNNG...</td>\n",
1138 |               "    </tr>\n",
1139 |               "    <tr>\n",
1140 |               "      <th>2</th>\n",
1141 |               "      <td>L</td>\n",
1142 |               "      <td>V</td>\n",
1143 |               "      <td>AAAAGTAAACATTTTCAATAAGAAAATACAAGACCCATACCGAAAG...</td>\n",
1144 |               "    </tr>\n",
1145 |               "    <tr>\n",
1146 |               "      <th>3</th>\n",
1147 |               "      <td>L</td>\n",
1148 |               "      <td>V</td>\n",
1149 |               "      <td>NNAAGTAAANNNNTNNAATAANAAAATACAAGACCCATNCCGAAAG...</td>\n",
1150 |               "    </tr>\n",
1151 |               "    <tr>\n",
1152 |               "      <th>4</th>\n",
1153 |               "      <td>F</td>\n",
1154 |               "      <td>Y</td>\n",
1155 |               "      <td>AATAAGAAAANNNNNNNNNNNNNNCGNAAGTTTNTTNNNNANAAAA...</td>\n",
1156 |               "    </tr>\n",
1157 |               "    <tr>\n",
1158 |               "      <th>...</th>\n",
1159 |               "      <td>...</td>\n",
1160 |               "      <td>...</td>\n",
1161 |               "      <td>...</td>\n",
1162 |               "    </tr>\n",
1163 |               "    <tr>\n",
1164 |               "      <th>95</th>\n",
1165 |               "      <td>K</td>\n",
1166 |               "      <td>M</td>\n",
1167 |               "      <td>TATAACAATTGTGAAATCTCTTGCTATTTTTATAAATGATTTTGAA...</td>\n",
1168 |               "    </tr>\n",
1169 |               "    <tr>\n",
1170 |               "      <th>96</th>\n",
1171 |               "      <td>Y</td>\n",
1172 |               "      <td>F</td>\n",
1173 |               "      <td>CAATTGTGAAATCTCTTGCTATTTTTATAAATGATTTTGAAGTTGA...</td>\n",
1174 |               "    </tr>\n",
1175 |               "    <tr>\n",
1176 |               "      <th>97</th>\n",
1177 |               "      <td>-</td>\n",
1178 |               "      <td>-</td>\n",
1179 |               "      <td>-</td>\n",
1180 |               "    </tr>\n",
1181 |               "    <tr>\n",
1182 |               "      <th>98</th>\n",
1183 |               "      <td>-</td>\n",
1184 |               "      <td>-</td>\n",
1185 |               "      <td>-</td>\n",
1186 |               "    </tr>\n",
1187 |               "    <tr>\n",
1188 |               "      <th>99</th>\n",
1189 |               "      <td>-</td>\n",
1190 |               "      <td>-</td>\n",
1191 |               "      <td>-</td>\n",
1192 |               "    </tr>\n",
1193 |               "  </tbody>\n",
1194 |               "</table>\n",
1195 |               "<p>100 rows × 3 columns</p>\n",
1196 |               "</div>\n",
1197 |               "    <div class=\"colab-df-buttons\">\n",
1198 |               "\n",
1199 |               "  <div class=\"colab-df-container\">\n",
1200 |               "    <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-feee07ef-00cd-413a-b52d-f5afaa83663d')\"\n",
1201 |               "            title=\"Convert this dataframe to an interactive table.\"\n",
1202 |               "            style=\"display:none;\">\n",
1203 |               "\n",
1204 |               "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\" viewBox=\"0 -960 960 960\">\n",
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1206 |               "  </svg>\n",
1207 |               "    </button>\n",
1208 |               "\n",
1209 |               "  <style>\n",
1210 |               "    .colab-df-container {\n",
1211 |               "      display:flex;\n",
1212 |               "      gap: 12px;\n",
1213 |               "    }\n",
1214 |               "\n",
1215 |               "    .colab-df-convert {\n",
1216 |               "      background-color: #E8F0FE;\n",
1217 |               "      border: none;\n",
1218 |               "      border-radius: 50%;\n",
1219 |               "      cursor: pointer;\n",
1220 |               "      display: none;\n",
1221 |               "      fill: #1967D2;\n",
1222 |               "      height: 32px;\n",
1223 |               "      padding: 0 0 0 0;\n",
1224 |               "      width: 32px;\n",
1225 |               "    }\n",
1226 |               "\n",
1227 |               "    .colab-df-convert:hover {\n",
1228 |               "      background-color: #E2EBFA;\n",
1229 |               "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
1230 |               "      fill: #174EA6;\n",
1231 |               "    }\n",
1232 |               "\n",
1233 |               "    .colab-df-buttons div {\n",
1234 |               "      margin-bottom: 4px;\n",
1235 |               "    }\n",
1236 |               "\n",
1237 |               "    [theme=dark] .colab-df-convert {\n",
1238 |               "      background-color: #3B4455;\n",
1239 |               "      fill: #D2E3FC;\n",
1240 |               "    }\n",
1241 |               "\n",
1242 |               "    [theme=dark] .colab-df-convert:hover {\n",
1243 |               "      background-color: #434B5C;\n",
1244 |               "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
1245 |               "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
1246 |               "      fill: #FFFFFF;\n",
1247 |               "    }\n",
1248 |               "  </style>\n",
1249 |               "\n",
1250 |               "    <script>\n",
1251 |               "      const buttonEl =\n",
1252 |               "        document.querySelector('#df-feee07ef-00cd-413a-b52d-f5afaa83663d button.colab-df-convert');\n",
1253 |               "      buttonEl.style.display =\n",
1254 |               "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
1255 |               "\n",
1256 |               "      async function convertToInteractive(key) {\n",
1257 |               "        const element = document.querySelector('#df-feee07ef-00cd-413a-b52d-f5afaa83663d');\n",
1258 |               "        const dataTable =\n",
1259 |               "          await google.colab.kernel.invokeFunction('convertToInteractive',\n",
1260 |               "                                                    [key], {});\n",
1261 |               "        if (!dataTable) return;\n",
1262 |               "\n",
1263 |               "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
1264 |               "          '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
1265 |               "          + ' to learn more about interactive tables.';\n",
1266 |               "        element.innerHTML = '';\n",
1267 |               "        dataTable['output_type'] = 'display_data';\n",
1268 |               "        await google.colab.output.renderOutput(dataTable, element);\n",
1269 |               "        const docLink = document.createElement('div');\n",
1270 |               "        docLink.innerHTML = docLinkHtml;\n",
1271 |               "        element.appendChild(docLink);\n",
1272 |               "      }\n",
1273 |               "    </script>\n",
1274 |               "  </div>\n",
1275 |               "\n",
1276 |               "\n",
1277 |               "    <div id=\"df-97e68d56-559f-4227-999b-18d525167ff4\">\n",
1278 |               "      <button class=\"colab-df-quickchart\" onclick=\"quickchart('df-97e68d56-559f-4227-999b-18d525167ff4')\"\n",
1279 |               "                title=\"Suggest charts\"\n",
1280 |               "                style=\"display:none;\">\n",
1281 |               "\n",
1282 |               "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
1283 |               "     width=\"24px\">\n",
1284 |               "    <g>\n",
1285 |               "        <path d=\"M19 3H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2zM9 17H7v-7h2v7zm4 0h-2V7h2v10zm4 0h-2v-4h2v4z\"/>\n",
1286 |               "    </g>\n",
1287 |               "</svg>\n",
1288 |               "      </button>\n",
1289 |               "\n",
1290 |               "<style>\n",
1291 |               "  .colab-df-quickchart {\n",
1292 |               "      --bg-color: #E8F0FE;\n",
1293 |               "      --fill-color: #1967D2;\n",
1294 |               "      --hover-bg-color: #E2EBFA;\n",
1295 |               "      --hover-fill-color: #174EA6;\n",
1296 |               "      --disabled-fill-color: #AAA;\n",
1297 |               "      --disabled-bg-color: #DDD;\n",
1298 |               "  }\n",
1299 |               "\n",
1300 |               "  [theme=dark] .colab-df-quickchart {\n",
1301 |               "      --bg-color: #3B4455;\n",
1302 |               "      --fill-color: #D2E3FC;\n",
1303 |               "      --hover-bg-color: #434B5C;\n",
1304 |               "      --hover-fill-color: #FFFFFF;\n",
1305 |               "      --disabled-bg-color: #3B4455;\n",
1306 |               "      --disabled-fill-color: #666;\n",
1307 |               "  }\n",
1308 |               "\n",
1309 |               "  .colab-df-quickchart {\n",
1310 |               "    background-color: var(--bg-color);\n",
1311 |               "    border: none;\n",
1312 |               "    border-radius: 50%;\n",
1313 |               "    cursor: pointer;\n",
1314 |               "    display: none;\n",
1315 |               "    fill: var(--fill-color);\n",
1316 |               "    height: 32px;\n",
1317 |               "    padding: 0;\n",
1318 |               "    width: 32px;\n",
1319 |               "  }\n",
1320 |               "\n",
1321 |               "  .colab-df-quickchart:hover {\n",
1322 |               "    background-color: var(--hover-bg-color);\n",
1323 |               "    box-shadow: 0 1px 2px rgba(60, 64, 67, 0.3), 0 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
1324 |               "    fill: var(--button-hover-fill-color);\n",
1325 |               "  }\n",
1326 |               "\n",
1327 |               "  .colab-df-quickchart-complete:disabled,\n",
1328 |               "  .colab-df-quickchart-complete:disabled:hover {\n",
1329 |               "    background-color: var(--disabled-bg-color);\n",
1330 |               "    fill: var(--disabled-fill-color);\n",
1331 |               "    box-shadow: none;\n",
1332 |               "  }\n",
1333 |               "\n",
1334 |               "  .colab-df-spinner {\n",
1335 |               "    border: 2px solid var(--fill-color);\n",
1336 |               "    border-color: transparent;\n",
1337 |               "    border-bottom-color: var(--fill-color);\n",
1338 |               "    animation:\n",
1339 |               "      spin 1s steps(1) infinite;\n",
1340 |               "  }\n",
1341 |               "\n",
1342 |               "  @keyframes spin {\n",
1343 |               "    0% {\n",
1344 |               "      border-color: transparent;\n",
1345 |               "      border-bottom-color: var(--fill-color);\n",
1346 |               "      border-left-color: var(--fill-color);\n",
1347 |               "    }\n",
1348 |               "    20% {\n",
1349 |               "      border-color: transparent;\n",
1350 |               "      border-left-color: var(--fill-color);\n",
1351 |               "      border-top-color: var(--fill-color);\n",
1352 |               "    }\n",
1353 |               "    30% {\n",
1354 |               "      border-color: transparent;\n",
1355 |               "      border-left-color: var(--fill-color);\n",
1356 |               "      border-top-color: var(--fill-color);\n",
1357 |               "      border-right-color: var(--fill-color);\n",
1358 |               "    }\n",
1359 |               "    40% {\n",
1360 |               "      border-color: transparent;\n",
1361 |               "      border-right-color: var(--fill-color);\n",
1362 |               "      border-top-color: var(--fill-color);\n",
1363 |               "    }\n",
1364 |               "    60% {\n",
1365 |               "      border-color: transparent;\n",
1366 |               "      border-right-color: var(--fill-color);\n",
1367 |               "    }\n",
1368 |               "    80% {\n",
1369 |               "      border-color: transparent;\n",
1370 |               "      border-right-color: var(--fill-color);\n",
1371 |               "      border-bottom-color: var(--fill-color);\n",
1372 |               "    }\n",
1373 |               "    90% {\n",
1374 |               "      border-color: transparent;\n",
1375 |               "      border-bottom-color: var(--fill-color);\n",
1376 |               "    }\n",
1377 |               "  }\n",
1378 |               "</style>\n",
1379 |               "\n",
1380 |               "      <script>\n",
1381 |               "        async function quickchart(key) {\n",
1382 |               "          const quickchartButtonEl =\n",
1383 |               "            document.querySelector('#' + key + ' button');\n",
1384 |               "          quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
1385 |               "          quickchartButtonEl.classList.add('colab-df-spinner');\n",
1386 |               "          try {\n",
1387 |               "            const charts = await google.colab.kernel.invokeFunction(\n",
1388 |               "                'suggestCharts', [key], {});\n",
1389 |               "          } catch (error) {\n",
1390 |               "            console.error('Error during call to suggestCharts:', error);\n",
1391 |               "          }\n",
1392 |               "          quickchartButtonEl.classList.remove('colab-df-spinner');\n",
1393 |               "          quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
1394 |               "        }\n",
1395 |               "        (() => {\n",
1396 |               "          let quickchartButtonEl =\n",
1397 |               "            document.querySelector('#df-97e68d56-559f-4227-999b-18d525167ff4 button');\n",
1398 |               "          quickchartButtonEl.style.display =\n",
1399 |               "            google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
1400 |               "        })();\n",
1401 |               "      </script>\n",
1402 |               "    </div>\n",
1403 |               "\n",
1404 |               "  <div id=\"id_340d86bf-d495-44c4-b208-970e606b5668\">\n",
1405 |               "    <style>\n",
1406 |               "      .colab-df-generate {\n",
1407 |               "        background-color: #E8F0FE;\n",
1408 |               "        border: none;\n",
1409 |               "        border-radius: 50%;\n",
1410 |               "        cursor: pointer;\n",
1411 |               "        display: none;\n",
1412 |               "        fill: #1967D2;\n",
1413 |               "        height: 32px;\n",
1414 |               "        padding: 0 0 0 0;\n",
1415 |               "        width: 32px;\n",
1416 |               "      }\n",
1417 |               "\n",
1418 |               "      .colab-df-generate:hover {\n",
1419 |               "        background-color: #E2EBFA;\n",
1420 |               "        box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
1421 |               "        fill: #174EA6;\n",
1422 |               "      }\n",
1423 |               "\n",
1424 |               "      [theme=dark] .colab-df-generate {\n",
1425 |               "        background-color: #3B4455;\n",
1426 |               "        fill: #D2E3FC;\n",
1427 |               "      }\n",
1428 |               "\n",
1429 |               "      [theme=dark] .colab-df-generate:hover {\n",
1430 |               "        background-color: #434B5C;\n",
1431 |               "        box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
1432 |               "        filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
1433 |               "        fill: #FFFFFF;\n",
1434 |               "      }\n",
1435 |               "    </style>\n",
1436 |               "    <button class=\"colab-df-generate\" onclick=\"generateWithVariable('results')\"\n",
1437 |               "            title=\"Generate code using this dataframe.\"\n",
1438 |               "            style=\"display:none;\">\n",
1439 |               "\n",
1440 |               "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
1441 |               "       width=\"24px\">\n",
1442 |               "    <path d=\"M7,19H8.4L18.45,9,17,7.55,7,17.6ZM5,21V16.75L18.45,3.32a2,2,0,0,1,2.83,0l1.4,1.43a1.91,1.91,0,0,1,.58,1.4,1.91,1.91,0,0,1-.58,1.4L9.25,21ZM18.45,9,17,7.55Zm-12,3A5.31,5.31,0,0,0,4.9,8.1,5.31,5.31,0,0,0,1,6.5,5.31,5.31,0,0,0,4.9,4.9,5.31,5.31,0,0,0,6.5,1,5.31,5.31,0,0,0,8.1,4.9,5.31,5.31,0,0,0,12,6.5,5.46,5.46,0,0,0,6.5,12Z\"/>\n",
1443 |               "  </svg>\n",
1444 |               "    </button>\n",
1445 |               "    <script>\n",
1446 |               "      (() => {\n",
1447 |               "      const buttonEl =\n",
1448 |               "        document.querySelector('#id_340d86bf-d495-44c4-b208-970e606b5668 button.colab-df-generate');\n",
1449 |               "      buttonEl.style.display =\n",
1450 |               "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
1451 |               "\n",
1452 |               "      buttonEl.onclick = () => {\n",
1453 |               "        google.colab.notebook.generateWithVariable('results');\n",
1454 |               "      }\n",
1455 |               "      })();\n",
1456 |               "    </script>\n",
1457 |               "  </div>\n",
1458 |               "\n",
1459 |               "    </div>\n",
1460 |               "  </div>\n"
1461 |             ],
1462 |             "application/vnd.google.colaboratory.intrinsic+json": {
1463 |               "type": "dataframe",
1464 |               "variable_name": "results",
1465 |               "summary": "{\n  \"name\": \"results\",\n  \"rows\": 100,\n  \"fields\": [\n    {\n      \"column\": \"reference_aa\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 9,\n        \"samples\": [\n          \"Y\",\n          \"F\",\n          \"S\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"variant_aa\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 12,\n        \"samples\": [\n          \"M\",\n          \"R\",\n          \"V\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"snp_centered_dna_window\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 50,\n        \"samples\": [\n          \"AAAAAAAAATGTTTNGAACTGTTTCATGATAATGATAACNAAAAAAGTTTTTGCTTTCTTNTTTTTTTTCCTCCGCAAAACAGTCTNAAAGTATAACCAAAAAGCCTATAAATCAATATAATTTGTTGTTTTGATTTACGTTTTACAGAAAATGGCGTTACAAAACAAAGAAGAAGAGAAAAAGAAAGTGNNNNNNNNGCAAAAGAGTTACTTCGNNNNNNNNGGAATCTGTTGTACATCGGAAGTTCCTATAATCAAGAATATTCTCAAGTCACTTGACGGCGTTAAAGAATATTCCGTCATCGTTCCCTCGAGAACCGTGATTGTTGTTCACGACAGTCTCCTCANCTCTCCCTTCCAAATTGGTAAATNTTTTTTTTCTTTGNGATAATAAANNTTTTTTNNNNNNNAAANATTGGTAAATCATTATAANTAAATAGTTATTTAANATTTCTCTAATTTTTAATTTTACTCAGTNAAAAAATAANAATTAANNNNNNTAAANAATTATTT\",\n          \"TGGAGGCAGCAGCAGTTGTGTTTCTGTTCACCATATCCGACTGGCTCGAAACAAGAGCTAGCTACAAGGNTTGTNTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGTGAAATTNAAACTATAATGGTTTATTAAGGTAATGATTATTGCAAATGTAAAATCTCAGGCGACCTCGGTAATGCAGTCTTTGATGAGCTTAGCTCCACAAAAGGCTACAATAGCAGAGACTGGTGAAGAAGTTGAGGTAGATGAGGTTAAGGTTGATACTGTTGTAGCAGTTAAAGCTGGTGAAACCATACCAATTGATGGGATTGTGGTGGATGGAAACTGTGAAGTAGACGAGAAAACCTTAACGGGCGAAGCATTTCCTGTGCCTAAACAGAGAGATTCTACGGTTTGGGCTGGCACCATCAATCTAAATGGTANGTAATCCTATTTTAAGAGCTTCAAGCTTTATACATTTTTGTTGTAT\",\n          \"CATTTTCCTCACTTGCAAATATATTTTAANAAATCTTCTTCCACCTTTGTTAATTAATGATTTAATTCTGAAAAACANTGTGTTGCAGCTAAGGCACTAAACGAAGCTAGGTTAGAAGCAAACGTGAGGGTAAACGGAGAAACTAGCTTCAAGAACAAATGGCCGAGCCCTTTCGCCGTAGTTTCCGGCTTACTTCTCCTCCTATCCTTCCTAAAGTTTGTCTACTCGCNTTTACGTTGGNTCGCCGTCGCAGCAGCTGCCGCCGGTNTNTNTCCGATTCTTGCCAAAGCCTTTGCTTCCATTAAAAGGCCTAGGATCGACATCAACATATTGGTCATAATAACCGGTAATACCACTTTCTCCTCTTTTCTTTATGCTGTCGTTATACCANTTTTTTTTNTAGTATTCATTATTAGCATCTAACATTATTTCTCTATATTACTCCGTGACTTAAGAATGATGTGTTCTATAATAATTTGTTAGTTTATGGNTTATCCGTGATCGATGTAACAA\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
1466 |             }
1467 |           },
1468 |           "metadata": {},
1469 |           "execution_count": 144
1470 |         }
1471 |       ]
1472 |     },
1473 |     {
1474 |       "cell_type": "code",
1475 |       "source": [
1476 |         "(results[\"reference_aa\"] == \"-\").sum()"
1477 |       ],
1478 |       "metadata": {
1479 |         "colab": {
1480 |           "base_uri": "https://localhost:8080/"
1481 |         },
1482 |         "id": "xNoABL4t0bZk",
1483 |         "outputId": "29585018-1d3f-46a2-952d-9df5a8cd5373"
1484 |       },
1485 |       "execution_count": null,
1486 |       "outputs": [
1487 |         {
1488 |           "output_type": "execute_result",
1489 |           "data": {
1490 |             "text/plain": [
1491 |               "np.int64(51)"
1492 |             ]
1493 |           },
1494 |           "metadata": {},
1495 |           "execution_count": 148
1496 |         }
1497 |       ]
1498 |     },
1499 |     {
1500 |       "cell_type": "code",
1501 |       "source": [
1502 |         "from google.colab import files\n",
1503 |         "results.to_csv(\"results.csv\", index=False)\n",
1504 |         "files.download(\"results.csv\")"
1505 |       ],
1506 |       "metadata": {
1507 |         "colab": {
1508 |           "base_uri": "https://localhost:8080/",
1509 |           "height": 17
1510 |         },
1511 |         "id": "xpN0OV2XwoKT",
1512 |         "outputId": "ced13f2c-b173-401c-ec77-db778519cbc2"
1513 |       },
1514 |       "execution_count": null,
1515 |       "outputs": [
1516 |         {
1517 |           "output_type": "display_data",
1518 |           "data": {
1519 |             "text/plain": [
1520 |               "<IPython.core.display.Javascript object>"
1521 |             ],
1522 |             "application/javascript": [
1523 |               "\n",
1524 |               "    async function download(id, filename, size) {\n",
1525 |               "      if (!google.colab.kernel.accessAllowed) {\n",
1526 |               "        return;\n",
1527 |               "      }\n",
1528 |               "      const div = document.createElement('div');\n",
1529 |               "      const label = document.createElement('label');\n",
1530 |               "      label.textContent = `Downloading \"${filename}\": `;\n",
1531 |               "      div.appendChild(label);\n",
1532 |               "      const progress = document.createElement('progress');\n",
1533 |               "      progress.max = size;\n",
1534 |               "      div.appendChild(progress);\n",
1535 |               "      document.body.appendChild(div);\n",
1536 |               "\n",
1537 |               "      const buffers = [];\n",
1538 |               "      let downloaded = 0;\n",
1539 |               "\n",
1540 |               "      const channel = await google.colab.kernel.comms.open(id);\n",
1541 |               "      // Send a message to notify the kernel that we're ready.\n",
1542 |               "      channel.send({})\n",
1543 |               "\n",
1544 |               "      for await (const message of channel.messages) {\n",
1545 |               "        // Send a message to notify the kernel that we're ready.\n",
1546 |               "        channel.send({})\n",
1547 |               "        if (message.buffers) {\n",
1548 |               "          for (const buffer of message.buffers) {\n",
1549 |               "            buffers.push(buffer);\n",
1550 |               "            downloaded += buffer.byteLength;\n",
1551 |               "            progress.value = downloaded;\n",
1552 |               "          }\n",
1553 |               "        }\n",
1554 |               "      }\n",
1555 |               "      const blob = new Blob(buffers, {type: 'application/binary'});\n",
1556 |               "      const a = document.createElement('a');\n",
1557 |               "      a.href = window.URL.createObjectURL(blob);\n",
1558 |               "      a.download = filename;\n",
1559 |               "      div.appendChild(a);\n",
1560 |               "      a.click();\n",
1561 |               "      div.remove();\n",
1562 |               "    }\n",
1563 |               "  "
1564 |             ]
1565 |           },
1566 |           "metadata": {}
1567 |         },
1568 |         {
1569 |           "output_type": "display_data",
1570 |           "data": {
1571 |             "text/plain": [
1572 |               "<IPython.core.display.Javascript object>"
1573 |             ],
1574 |             "application/javascript": [
1575 |               "download(\"download_d7f10122-a0c2-4540-863a-4cf24d73e405\", \"results.csv\", 25736)"
1576 |             ]
1577 |           },
1578 |           "metadata": {}
1579 |         }
1580 |       ]
1581 |     },
1582 |     {
1583 |       "cell_type": "code",
1584 |       "source": [
1585 |         "results[\"snp_centered_dna_window\"].apply(lambda x: len(x))"
1586 |       ],
1587 |       "metadata": {
1588 |         "colab": {
1589 |           "base_uri": "https://localhost:8080/",
1590 |           "height": 147
1591 |         },
1592 |         "id": "1alzRqCgu_RZ",
1593 |         "outputId": "2b546112-5323-4799-a5bd-9019be3fc192"
1594 |       },
1595 |       "execution_count": null,
1596 |       "outputs": [
1597 |         {
1598 |           "output_type": "execute_result",
1599 |           "data": {
1600 |             "text/plain": [
1601 |               "0    513\n",
1602 |               "1    513\n",
1603 |               "Name: snp_centered_dna_window, dtype: int64"
1604 |             ],
1605 |             "text/html": [
1606 |               "<div>\n",
1607 |               "<style scoped>\n",
1608 |               "    .dataframe tbody tr th:only-of-type {\n",
1609 |               "        vertical-align: middle;\n",
1610 |               "    }\n",
1611 |               "\n",
1612 |               "    .dataframe tbody tr th {\n",
1613 |               "        vertical-align: top;\n",
1614 |               "    }\n",
1615 |               "\n",
1616 |               "    .dataframe thead th {\n",
1617 |               "        text-align: right;\n",
1618 |               "    }\n",
1619 |               "</style>\n",
1620 |               "<table border=\"1\" class=\"dataframe\">\n",
1621 |               "  <thead>\n",
1622 |               "    <tr style=\"text-align: right;\">\n",
1623 |               "      <th></th>\n",
1624 |               "      <th>snp_centered_dna_window</th>\n",
1625 |               "    </tr>\n",
1626 |               "  </thead>\n",
1627 |               "  <tbody>\n",
1628 |               "    <tr>\n",
1629 |               "      <th>0</th>\n",
1630 |               "      <td>513</td>\n",
1631 |               "    </tr>\n",
1632 |               "    <tr>\n",
1633 |               "      <th>1</th>\n",
1634 |               "      <td>513</td>\n",
1635 |               "    </tr>\n",
1636 |               "  </tbody>\n",
1637 |               "</table>\n",
1638 |               "</div><br><label><b>dtype:</b> int64</label>"
1639 |             ]
1640 |           },
1641 |           "metadata": {},
1642 |           "execution_count": 127
1643 |         }
1644 |       ]
1645 |     },
1646 |     {
1647 |       "cell_type": "code",
1648 |       "source": [],
1649 |       "metadata": {
1650 |         "id": "CuUvWfMpvwOz"
1651 |       },
1652 |       "execution_count": null,
1653 |       "outputs": []
1654 |     },
1655 |     {
1656 |       "cell_type": "code",
1657 |       "source": [
1658 |         "first_result = df.loc[4].to_dict()\n",
1659 |         "first_result"
1660 |       ],
1661 |       "metadata": {
1662 |         "colab": {
1663 |           "base_uri": "https://localhost:8080/"
1664 |         },
1665 |         "id": "0AOlo1ha2e1d",
1666 |         "outputId": "ace84581-4489-425a-88aa-d4acec34bab3"
1667 |       },
1668 |       "execution_count": null,
1669 |       "outputs": [
1670 |         {
1671 |           "output_type": "execute_result",
1672 |           "data": {
1673 |             "text/plain": [
1674 |               "{'chromosome': 2,\n",
1675 |               " 'position': 8279539,\n",
1676 |               " 'accession': 9525,\n",
1677 |               " 'reference': 'T',\n",
1678 |               " 'variant': 'A',\n",
1679 |               " '-': 40,\n",
1680 |               " 'impacts': 'MODERATE',\n",
1681 |               " 'effects': 'missense_variant'}"
1682 |             ]
1683 |           },
1684 |           "metadata": {},
1685 |           "execution_count": 59
1686 |         }
1687 |       ]
1688 |     },
1689 |     {
1690 |       "cell_type": "code",
1691 |       "source": [
1692 |         "get_accession_gene_fasta(HMA4_gene_id)(first_result[\"accession\"])"
1693 |       ],
1694 |       "metadata": {
1695 |         "colab": {
1696 |           "base_uri": "https://localhost:8080/",
1697 |           "height": 140
1698 |         },
1699 |         "id": "b1UmpkUTq3yG",
1700 |         "outputId": "36e61bb1-c3cc-4731-9064-6865e209bd31"
1701 |       },
1702 |       "execution_count": null,
1703 |       "outputs": [
1704 |         {
1705 |           "output_type": "execute_result",
1706 |           "data": {
1707 |             "text/plain": [
1708 |               "'>MPI-GMI|Ath-1001-Genomes|pseudo-genome|9525|Chr2:8278881..8286445|Col-0_gi:AT2G19110.1|V0.2\\nCTACGTTCCTAACACTTCTCTCAACCTTTATCTGATCGCACCAAACCAGTTTTTTCGCATCGGCTNCTTCCTTTTGCTACTAGCTCTCCTCTCTTCTCCGGTNTTTTTGTCTCNCTTCTTAATTCACACAGATTTCATGATAAGTGATGATCTATAACAAGACGCTAACTCTTCTCTTGCATTTCTCGTGTTTTCATTTTCTTGTTACGCCAAATTTATCCCTTCAAAATCNNTTTTTTATGNGTATAGAATCCAAATAATAAGTAAAAGCTGATTCGTCTTCTTCCACTTAACACAAGTAAGCAGTGAGAGGGTGAAGATTTTTCTTTAGGAAAACAAAGAGAGTGAAGATATTTTTTGGCTTGATCTCAACATTATTTTTTCNTAAAAGTAAACATTTTCAATAAGAAAANNNNNNNNNNNNNNCGNAAGTTTNTTNNNNANAAAAAAAAAAAGGNTTTGANCTGTTTCATGATAATGATAACNAAAAAAGTTTTTGCTTTCTTNTTTTTTTTCCTCCGCAAAACAGTCTNAAAGTATAACCAAAAAGCCTATAAATCAATATAATTTGTTGTTTTGATTTACGTTTTACNGAAAATGGCGTTACAAAACAAAGAAGAAGAGAAAAAGAAAGTGAAGAAGTTGCAAAAGAGTTACTACGATGTTCTCGGAATCTGTTGTACATCGGAAGTTCCTATAATCGAGAATATTCTCAAGTCACTTGACGGCGTTAAAGAATATTCCGTCATCGTTCCCTCGAGAACCGTGNTTGTTGTTCACGACAGNNTCCTCATCTCTCCCTTCCNAATTGGTAAATNTTTTTTTTCTTTNTGATAATAAAGNTTTTTTNNNNNAAAAAAATTGGTAAATCATTATAANTAAATAGTTATTTAANATTTCTCTAATTTTTAATTTTACTCAGTNAAAAAATAANAATTAAAAAGCATAAATAANNNNNNNNTATTACACGAAAAGCTCACTTCATCTTATTTCTATTTATAAATTAGTGGTTTTGCGTCATGGTTTGATATTTTAATTAGTCAAATATATGTGATCCAANAAGTCACTTCAACTGAAAATATTTAATATTCTACCACTNAAATTTAATTTGCTTTCCCAAATCATTTCTTCTTAAGAAAACTAGTTTAGANCCAATTCTGTTTTANCAAAGTAATTTTTTCTTAATTGCTTTGCTTTGATATTTATGTACTGATNNNNNNNNNNNNNTGGTTGTNTTTTTAACCTAGGAGCTAAAGGNNAATATTAAAATTAACANTTTTTTCGCCTACAACAAAATAGGATAAACCGTTACTNTTTTTTNTGTTTTATTAATCCCATGAAACACGTTCAGTTAGNATAACCAAAGATTGTGAATAAGGTTCGTCTANTTTTTTTTCAAACTGTATCTAGTAAACCAACAAATTAAAAATGGTAACTTTTATAGAAACGCATAATGATACAATAACGGCAATAATACAACGAATCACATGTTTNTATAAATTCTAAATTTTGCATATCATAAAACCTTTACCACATTNNNTNTTTTNTGCATATTATAGCTAACCTAATACGTGCATATAACGCANNNTACGTGTGTAAACAAATAAATAATATATTTAATTGACATCATATATAGAATTTAATTCCGAAATCATATATAGATAATACATAATAGAANAAAGGTTGTTAGAAAAAGCCTGTCGTGATACTTTACCAAATCTTTTGATATGAATATTTAATTGGTAGTGCATCATACTCGTTACGTAACAATATTTTATAATTTTTATTTGACAGAAAACATATTCTATATTAGACATTNAAAGTNAAAAATAATCAAANAAAAAATCANAAAAAATTAAATAATAACACTATTTTCATCATTAAGAAAATACACTATTTTCAGTTTATTATNTANTAGTTTTTAAGGTTTGAATTTATAAAAATTGGCTAATATTTGTCATTTTCCTCACTTGCAAATATATTTTAANAAATCTTCTTCCACCTTTGTTAATTNATGATTTAATTCNGAAAAACANNGTGTTGCAGCNAAGGCACTAAACGAAGCTAGGTTAGNAGCAAANGTNAGGNTAAANGGAGAAACTAGCTTCAAGAACAAATGGCCGAGCCCTTTCGCCGTAGTTTCCGGCTTACTNCTCCTCCTATCCTTCCTAAAGTTTGTCTACNCNCNTTTACGTTGGCTCGCCGTCGCAGCAGTTGCCGCCGGTATCTATCCGATTCTTGCCAAAGCCTTTGCTTCCATTAAAAGGCCTAGGATCGACATCAACATATTGGTCATAATAACCGGTAATACCACTTTCTCCTCTTTTCTTTATGCTGTCGTTATACCANTTTTTTTTNTAGTATTCATTATTAGCATCTAACATTATTTCTCTATATTACTCCGTGACTTAAGAATGATGTGTTCTATAATAATTTGTTAGTTTATGGNTTATCCGTGATCGATGTAACAACTAGAAATAATATTGTTACTTATCTAAGATTTGNAAACTTAGCAAATTGTGGTTAAGGTAAAACTATTAATATATATAATTTCTTAAAANTTGTGATCGAGTCTCTATCCCTTTTTCGGTATTTTAAAAAAGCTTACATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAAAAGTTTCCTTTATTTTGTTCGTAACNTTTTTAAATAAATTCATATGGGAAAACTACTAAAGAATAGGTATTAAGAAAAATATTGTATTATGCTCAACTTATTTTACTGAACTCCAATATAGGAAAAATTAAATACGTGTAGCAGTTTGATATGNTTGTTATATTGTAGANTTTATTTGAGTTATAGGTTATAGAGGAAAACTAAAACAACTTTATATTTTTGCCGTAAGCAATGCAAATTNGAGTTATAGTTTATAGGAAAAAATNAAAATGTTCTTAGGATATAGGAAAAGTGAACATGTNATATAAACTTGAAAGTTGGTGTGGAAGATAATGCAAAAACAAAAGGTGCATTTCAAAATACGGGAAAAAGAAAGACGCCTTTCTCTTTTCTGTTTATAAAAATATACATTTTCGTTCATTTCTACTAGTACGATTATTTATAGGAACATACATAATTTCAAATTAAAACCATCTAAAGAGTAGNGAAAATAATTAAATATTTTGTTCAAGGAAAATAGTTATATTGTCTATAACGTAGGCAAGAAAATAAAAATCAGTTTTATTTTCCTNGGGTGCAATTAAGANGNCAATCTTTTTATATAAAATCAGAGTAATTTCATACCAGAAATCCAGACTAAATTTTGAGNTTTGTAGGAAGTCTCAAAAATCATAGTGTGATATCTTTTGATGNTTTTTTCTAAAACAATTACAATTACGTGCCATAGATAGAAAAACGCTAAGCATAGGTTTTTGATTGAAAATGGAAAATGGAAAAAGAACCTTCAACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGGAGCTATGGAATTAGTTTTAGTTGNANTTTCTGTTTAGTAGACATAATTAACAANAAACCATACAAAGTCATNTNNANCCAAGTTTTTTTTTTTTTNTNNTTTTTTTTTNTTTCGCTTGGTAGATGTTATAGTGTTACTTTAAGCTTTCTTTGATTTTCTAAAAACAAAATATTTTACACTGAGAGGTGATACAATGTTTTAGGTTTAAACTGATAATGATCCAATTTCTTCAATACAGTGATTGCAACACTTGCAATGCAAGATTTCATGGAGGCAGCAGCAGTTGTGTTCCTATTCACCATATCCGACTGGCTCGAAACAAGAGCTAGCTACAAGGNTTGTTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTGTGNNNNNNNNNNNNNNNTGGTNTANNNAGGTAATGATTATTGCAAATGTAAAATCTCAGGCGACCTCGGTAATGCAGTCTTTGATGAGCTTAGCTCCACAAAAGGCTACAATAGCAGAGACTGGTGAAGAAGTTGAGGTAGATGAGGTTAAGGTTGATACTGTTGTAGCAGTTAAAGCTGGTGAAACCATACCAATTGATGGGATTGTGGTGGATGGAAACTGTGAAGTAGACGAGAAAACCTTAACGGGCGAAGCATTTCCTGTGCCTAAACAGAGAGATTCTACGGTTTGGGCTGGNACCATCAATCTAAATGGTANGTAATCCTATTTTAAGAGCTTCAAGCTTTATACATTTTTGTTGTATCTTTCATTCTTTTGATCTTTCTTGGTNTTTTTTTTGCAGGTTACATAAGTGNGAAAACAACTTCTTTAGCGGGTGATTGCGTGGTTGCGAAAATGGCTAAGCTAGTAGAAGAAGCTCAGAGCAGTAAAACCAAATCTCAGAGACTAATAGACAAATGTTCTCAGTACTATACTCCAGGTAAGCAAAGACATAACCAAAACGTNNTNTTTATGTTCTTGATTCGAGTAATTTTGAGACCTCTGTGNTTCTTGTTTTGTTTTCAGCAATCATCTTAGTATCAGCTTGCGTCGCCATTGTCCCGGTTATAATGAAGGTCCACAACCTTAAACATTGGTTCCACCTAGCATTAGTTGTGTTAGTCAGTGGTTGTCCCTGTGGTCTTATCCTCTCTACACCAGTTGCTACTTTCTGTGCACTTACTAAAGCGGCAACTTCCGGACTTCTGATCAAAAGTGCTGATTATCTTGACACTCTCTCAAAGATCAAGATCGTTGCTTTCGATAAAACTGGGACTATTACAAGAGGAGAGTTNATTGTCATAGNTTTCAAGTCNCTCTCTAGAGATATAAACCNACGCAGCTTGCTTTNCTGGNNAAAAAAAAACTTGTGTNCTNNCCATAACNAGTTTGCCGAGATAACTTATGACNGAGACTTTCTTGTTATATAATGTTTCAGGGTATCTAGTGTTGAAAGCAAATCAAGTCATCCAATGGCTGCAACAATCGTGGACTATGCAAAATCTGTTTCTGTTGAGCCTAGGCCTGAAGAGGTTGAGGATTACCAGAACTTTCCAGGTGAAGGAATCTACGGGAAGATTGATGGTAACGATATCTTCATTGGGAACNAAAAGATTGCTTCTCGAGCTGGTTGTTCAACAGGTACTTGTAATATAAAGCTCAACAGAATGTTTTGAGGTCTTGGTATTCTTTAGTCTGAGCACTTGATTNTTCTTTCTTTACAGTTCCAGAGATTGAAGTTGATACCAAAGGCGGGAAGACTGTTGGATACGTCTATGTAGGTGAAAGACTAGCTGGATTTTTCAATCTTTCTGATGCTTGTAGATCTGGTGTTTCTCAAGCAATGGCAGAACTGAAATCTCTAGGAATCAAAACCGCAATGCTAACGGGAGATAATCAAGCCGCGGCAATGCATGCTCAAGAACAGGTGAGACTAATATAAACCATAATTTTAATCACTCTCTTAAGCGAAGACGTTGTTTAATAGTNCCTTGAAATGTCTTATGAAACAGCTAGGGAATGTTTTAGATGTTGTACATGGAGATCTTCTTCCAGAAGATAAGTCCAGAATCATACAAGAGTTTAAGAAAGAGGGACCAACCGCAATGGTAGGGGACGGTGTGAATGATGCACCAGCTTTAGCTACAGCTGATATTGGTATCTCCATGGGAATTTCTGGCTCTGCTCTTGCAACACAAACTGGTAATATTATTCTGATGTCTAATGATATAAGAAGGATACCACAAGCGGTGAAGCTAGCGAGAAGAGCACGACGCAAAGTTGTTGAAAACGTGTGTCTATCAATCATTTTAAAAGCAGGAATNCTCGCTTNGGCATTTGCTGGTCATCCTTTGATTTGGGCTGCGGTTCTTGTTGATGTAGGGACTTGTCTGCTTGTNATTTTCAATAGTATGTTGCTGCTGCGAGAGAAGAAAAAGATTGGGAACAAAAAGTGTTACAGGGCTTCTACATCTAAGTTGAATGGTAGGAAACTTGAAGGCGATGATGATTATGTTGTGGACTTAGANGCAGGCTTGTTAAAAAAGAGCGGGAATGGTCAATGCAAATCAAGCTGTTGTGGAGATAAGAAAAATCAAGAGAATGTTGTGATGATGAAACCAAGTAGTAAAACCAGTTCTGATCATTCTCACCCTGGTTGTTGTGGCGATAAGAAGGAAGAAAAAGTGAAGCCGCTTGTGAAAGATGGCTGTTGCAGTGAGAAAACTAGGAAACCAGAGGGAGATATGGTTTCATTGAGCTCATGTANGAAGTCTAGTCATGTNAAACATGACCTGAAAATGNAAGGTGGTTCAGGTTGTTGTGNTAGCAAAAATNAGNAAGNGAAGGAANTAGTAGCAAAAAGCTGTTGTGAGAAACCCAAACAGCAGGNGGNGAGNGTTNGAGACTGCAAGTCTGGTCATTGCGAGAAGAAGAAGCAAGCTGAAGACATTGTTGTCCCGGTGCAGATTATTGGTCATGCATTAACGCATGTGGAGATCGAGTTGCAGACAAAGGAAACCTGCAAAACAAGCTGTTGTGACAGTAAAGATAAGGTTAAGGAGACAGGTTTGCTGCTTTCTAGTGAGAACACNCCTTACCTGGAGAAAGGNGTGCTGATTAAAGATGAAGGAAACTGCAAGTCTGGCAGCGAGAACATGGGGACAGTGAAACAAAGCTGCCATGAGAAGGGCTGCAGCGATGANAAACAAACCGGGGAAATAACTCTTGCTTCGGAGGAAGAGACAGATGATCAAGATTGCTCCTCGGGATGTTGTGTGAACGAGGGAACAGTGAAACAAAGCTTCCATGAGAAGAAGCATTCTGTGTTGGTGGAGAAGGAAGGTTTGGACATGGAAACTGGTTTCTGTTGTGATGCCAAGCTGGTTTGTTGTGGAAACACAGAAGGTGAAGTGAAGGAGCAATGTCGTCTGGAGATAAAGAAAGAAGAACATTGCAAGTCTGGTTGCTGCGGCGAGGAAAAACAAACCGGAGAAATCGCTCTGGNTTCAGAGGAAGAGNNNNNNAGCACGAATTGTTCCACGGGTTGTTGTGTGGACAAAGAAGAAGTGACACAAACCTGTCATGAGAAGCCTGTTAGCTTGGTGGTATCAGGCTTGGAAGTGAAGAAGGATGAGCATTGTGAGAGCTCACACAGAGCCGTCAAGGTAGAGACCTGTTGCAAAGTGAAGATTCCAGAGGCTTGCGCATCAAAATGTAGGGACAGAGCGAAGCGTCACAGTGGTAAAAGCTGTTGCAGGAGTTATGCAAAAGAGNTATGCAGCCACCGCCATCATCATCACCACCACCACCACCATCACCATGTGAGTGCTTGATGGAGATTGATTGAATAACTTAAACTCTTGATGCATCCATCTATTCACATTACGTTTANTCTCATTCCGTGAATGCCGAAANAAAAAACAAAATGTTCCAGCAAAGGCAGTTTATTAGATTAAGCAACTGTGTTATTCATAAAGACAATGCTAGTGATTTTTTTTAAGTACTTTATGTATTGCAATTCCT'"
1709 |             ],
1710 |             "application/vnd.google.colaboratory.intrinsic+json": {
1711 |               "type": "string"
1712 |             }
1713 |           },
1714 |           "metadata": {},
1715 |           "execution_count": 87
1716 |         }
1717 |       ]
1718 |     },
1719 |     {
1720 |       "cell_type": "code",
1721 |       "source": [
1722 |         "HMA4_fasta_cache = DefaultDict(get_accession_gene_fasta(HMA4_gene_id))"
1723 |       ],
1724 |       "metadata": {
1725 |         "id": "vMJWm-_kqPJO"
1726 |       },
1727 |       "execution_count": null,
1728 |       "outputs": []
1729 |     },
1730 |     {
1731 |       "cell_type": "code",
1732 |       "source": [
1733 |         "get_aa_substitution_pair(first_result)"
1734 |       ],
1735 |       "metadata": {
1736 |         "colab": {
1737 |           "base_uri": "https://localhost:8080/"
1738 |         },
1739 |         "id": "uoAvXA5_l1W_",
1740 |         "outputId": "0f777d88-f870-4aae-c161-f6e57a9b8e4d"
1741 |       },
1742 |       "execution_count": null,
1743 |       "outputs": [
1744 |         {
1745 |           "output_type": "execute_result",
1746 |           "data": {
1747 |             "text/plain": [
1748 |               "(MutableSeq('Y'), MutableSeq('F'))"
1749 |             ]
1750 |           },
1751 |           "metadata": {},
1752 |           "execution_count": 61
1753 |         }
1754 |       ]
1755 |     },
1756 |     {
1757 |       "cell_type": "code",
1758 |       "source": [
1759 |         "fasta = get_accession_gene_fasta(first_result[\"accession\"], HMA4_gene_id)"
1760 |       ],
1761 |       "metadata": {
1762 |         "id": "JrsYwelu6CiX"
1763 |       },
1764 |       "execution_count": null,
1765 |       "outputs": []
1766 |     },
1767 |     {
1768 |       "cell_type": "code",
1769 |       "source": [
1770 |         "record = SeqIO.read(StringIO(fasta), \"fasta\")\n",
1771 |         "record"
1772 |       ],
1773 |       "metadata": {
1774 |         "colab": {
1775 |           "base_uri": "https://localhost:8080/"
1776 |         },
1777 |         "id": "DPj6gOYcbT3h",
1778 |         "outputId": "f74e2595-2953-4c15-8184-13fbc5a5a5aa"
1779 |       },
1780 |       "execution_count": null,
1781 |       "outputs": [
1782 |         {
1783 |           "output_type": "execute_result",
1784 |           "data": {
1785 |             "text/plain": [
1786 |               "SeqRecord(seq=Seq('CTACGTTCCTAACANTTCTCTCAACCTTTATCTGATCGCACCAAACCAGTTTTT...CCT'), id='MPI-GMI|Ath-1001-Genomes|pseudo-genome|9653|Chr2:8278881..8286445|Col-0_gi:AT2G19110.1|V0.2', name='MPI-GMI|Ath-1001-Genomes|pseudo-genome|9653|Chr2:8278881..8286445|Col-0_gi:AT2G19110.1|V0.2', description='MPI-GMI|Ath-1001-Genomes|pseudo-genome|9653|Chr2:8278881..8286445|Col-0_gi:AT2G19110.1|V0.2', dbxrefs=[])"
1787 |             ]
1788 |           },
1789 |           "metadata": {},
1790 |           "execution_count": 18
1791 |         }
1792 |       ]
1793 |     },
1794 |     {
1795 |       "cell_type": "code",
1796 |       "source": [
1797 |         "aa = record.seq.translate()"
1798 |       ],
1799 |       "metadata": {
1800 |         "colab": {
1801 |           "base_uri": "https://localhost:8080/"
1802 |         },
1803 |         "id": "Dlox9xZqdM-e",
1804 |         "outputId": "f8c7685c-967a-4055-d46d-6516cb5e66ff"
1805 |       },
1806 |       "execution_count": null,
1807 |       "outputs": [
1808 |         {
1809 |           "output_type": "stream",
1810 |           "name": "stderr",
1811 |           "text": [
1812 |             "/usr/local/lib/python3.12/dist-packages/Bio/Seq.py:2877: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n",
1813 |             "  warnings.warn(\n"
1814 |           ]
1815 |         }
1816 |       ]
1817 |     },
1818 |     {
1819 |       "cell_type": "code",
1820 |       "source": [
1821 |         "start, _ = get_start_end_from_seq(record)\n",
1822 |         "start"
1823 |       ],
1824 |       "metadata": {
1825 |         "colab": {
1826 |           "base_uri": "https://localhost:8080/"
1827 |         },
1828 |         "id": "0WZ4QyJSgohr",
1829 |         "outputId": "ba68e1fa-54e0-4243-f9c7-d7c5e1ccb845"
1830 |       },
1831 |       "execution_count": null,
1832 |       "outputs": [
1833 |         {
1834 |           "output_type": "execute_result",
1835 |           "data": {
1836 |             "text/plain": [
1837 |               "8278881"
1838 |             ]
1839 |           },
1840 |           "metadata": {},
1841 |           "execution_count": 37
1842 |         }
1843 |       ]
1844 |     },
1845 |     {
1846 |       "cell_type": "code",
1847 |       "source": [
1848 |         "in_gene_position = first_result[\"position\"] - start"
1849 |       ],
1850 |       "metadata": {
1851 |         "id": "XNRtQwOzeD9-"
1852 |       },
1853 |       "execution_count": null,
1854 |       "outputs": []
1855 |     },
1856 |     {
1857 |       "cell_type": "code",
1858 |       "source": [
1859 |         "first_result[\"variant\"] == record.seq[in_gene_position]"
1860 |       ],
1861 |       "metadata": {
1862 |         "colab": {
1863 |           "base_uri": "https://localhost:8080/"
1864 |         },
1865 |         "id": "xoJgVLKig9F5",
1866 |         "outputId": "5a7ca1b8-217f-4acf-ddaa-de3bee4009c9"
1867 |       },
1868 |       "execution_count": null,
1869 |       "outputs": [
1870 |         {
1871 |           "output_type": "execute_result",
1872 |           "data": {
1873 |             "text/plain": [
1874 |               "True"
1875 |             ]
1876 |           },
1877 |           "metadata": {},
1878 |           "execution_count": 47
1879 |         }
1880 |       ]
1881 |     },
1882 |     {
1883 |       "cell_type": "code",
1884 |       "source": [
1885 |         "codon_start = (in_gene_position // 3) * 3\n",
1886 |         "codon_start"
1887 |       ],
1888 |       "metadata": {
1889 |         "colab": {
1890 |           "base_uri": "https://localhost:8080/"
1891 |         },
1892 |         "id": "paV0Hfbah0Hy",
1893 |         "outputId": "7e18ef33-0e33-41d4-a476-6f9712c3b4e5"
1894 |       },
1895 |       "execution_count": null,
1896 |       "outputs": [
1897 |         {
1898 |           "output_type": "execute_result",
1899 |           "data": {
1900 |             "text/plain": [
1901 |               "642"
1902 |             ]
1903 |           },
1904 |           "metadata": {},
1905 |           "execution_count": 48
1906 |         }
1907 |       ]
1908 |     },
1909 |     {
1910 |       "cell_type": "code",
1911 |       "source": [
1912 |         "in_condon_position = in_gene_position % 3\n",
1913 |         "in_condon_position"
1914 |       ],
1915 |       "metadata": {
1916 |         "colab": {
1917 |           "base_uri": "https://localhost:8080/"
1918 |         },
1919 |         "id": "hpEdQDqAimqV",
1920 |         "outputId": "f3d3e3ca-39dc-48c7-d5b3-0665edd3dfcc"
1921 |       },
1922 |       "execution_count": null,
1923 |       "outputs": [
1924 |         {
1925 |           "output_type": "execute_result",
1926 |           "data": {
1927 |             "text/plain": [
1928 |               "0"
1929 |             ]
1930 |           },
1931 |           "metadata": {},
1932 |           "execution_count": 49
1933 |         }
1934 |       ]
1935 |     },
1936 |     {
1937 |       "cell_type": "code",
1938 |       "source": [
1939 |         "codon = MutableSeq(record.seq[codon_start:codon_start+3])"
1940 |       ],
1941 |       "metadata": {
1942 |         "id": "zY5RIgdMiI40"
1943 |       },
1944 |       "execution_count": null,
1945 |       "outputs": []
1946 |     },
1947 |     {
1948 |       "cell_type": "code",
1949 |       "source": [
1950 |         "codon.translate()"
1951 |       ],
1952 |       "metadata": {
1953 |         "colab": {
1954 |           "base_uri": "https://localhost:8080/"
1955 |         },
1956 |         "id": "cDkbbg01iQSp",
1957 |         "outputId": "9dd02500-7d28-43ba-f248-cda40a358fda"
1958 |       },
1959 |       "execution_count": null,
1960 |       "outputs": [
1961 |         {
1962 |           "output_type": "execute_result",
1963 |           "data": {
1964 |             "text/plain": [
1965 |               "MutableSeq('V')"
1966 |             ]
1967 |           },
1968 |           "metadata": {},
1969 |           "execution_count": 55
1970 |         }
1971 |       ]
1972 |     },
1973 |     {
1974 |       "cell_type": "code",
1975 |       "source": [
1976 |         "codon[in_condon_position] = first_result[\"reference\"]\n",
1977 |         "codon.translate()"
1978 |       ],
1979 |       "metadata": {
1980 |         "colab": {
1981 |           "base_uri": "https://localhost:8080/"
1982 |         },
1983 |         "id": "A7pDErOziTPs",
1984 |         "outputId": "98ba4e30-6be5-4e7d-b2a1-936bdacdbae0"
1985 |       },
1986 |       "execution_count": null,
1987 |       "outputs": [
1988 |         {
1989 |           "output_type": "execute_result",
1990 |           "data": {
1991 |             "text/plain": [
1992 |               "MutableSeq('L')"
1993 |             ]
1994 |           },
1995 |           "metadata": {},
1996 |           "execution_count": 56
1997 |         }
1998 |       ]
1999 |     },
2000 |     {
2001 |       "cell_type": "code",
2002 |       "source": [
2003 |         "aa"
2004 |       ],
2005 |       "metadata": {
2006 |         "colab": {
2007 |           "base_uri": "https://localhost:8080/"
2008 |         },
2009 |         "id": "41MMMDoweAtl",
2010 |         "outputId": "45777d91-ac38-4a1e-9d9e-b85bf4dce3af"
2011 |       },
2012 |       "execution_count": null,
2013 |       "outputs": [
2014 |         {
2015 |           "output_type": "execute_result",
2016 |           "data": {
2017 |             "text/plain": [
2018 |               "Seq('LRS*XFSQPLSDRTKPVFSHRLLPFAXSSPLFSGXFVSLLNSHRFHDK**SIXR...CNS')"
2019 |             ]
2020 |           },
2021 |           "metadata": {},
2022 |           "execution_count": 22
2023 |         }
2024 |       ]
2025 |     },
2026 |     {
2027 |       "cell_type": "code",
2028 |       "source": [
2029 |         "record.id"
2030 |       ],
2031 |       "metadata": {
2032 |         "colab": {
2033 |           "base_uri": "https://localhost:8080/",
2034 |           "height": 35
2035 |         },
2036 |         "id": "c4EnAyO0fxGy",
2037 |         "outputId": "cbc2bd94-3564-45cb-e5d8-883c261db2fe"
2038 |       },
2039 |       "execution_count": null,
2040 |       "outputs": [
2041 |         {
2042 |           "output_type": "execute_result",
2043 |           "data": {
2044 |             "text/plain": [
2045 |               "'MPI-GMI|Ath-1001-Genomes|pseudo-genome|9653|Chr2:8278881..8286445|Col-0_gi:AT2G19110.1|V0.2'"
2046 |             ],
2047 |             "application/vnd.google.colaboratory.intrinsic+json": {
2048 |               "type": "string"
2049 |             }
2050 |           },
2051 |           "metadata": {},
2052 |           "execution_count": 31
2053 |         }
2054 |       ]
2055 |     },
2056 |     {
2057 |       "cell_type": "code",
2058 |       "source": [
2059 |         "record.seq[in_gene_position]"
2060 |       ],
2061 |       "metadata": {
2062 |         "colab": {
2063 |           "base_uri": "https://localhost:8080/",
2064 |           "height": 35
2065 |         },
2066 |         "id": "-y8MHPRrndYi",
2067 |         "outputId": "78cdd7ef-10e0-4e3e-80db-eb2351c60ad3"
2068 |       },
2069 |       "execution_count": null,
2070 |       "outputs": [
2071 |         {
2072 |           "output_type": "execute_result",
2073 |           "data": {
2074 |             "text/plain": [
2075 |               "'G'"
2076 |             ],
2077 |             "application/vnd.google.colaboratory.intrinsic+json": {
2078 |               "type": "string"
2079 |             }
2080 |           },
2081 |           "metadata": {},
2082 |           "execution_count": 63
2083 |         }
2084 |       ]
2085 |     },
2086 |     {
2087 |       "cell_type": "code",
2088 |       "source": [
2089 |         "snp_centered_dna_window = record.seq[in_gene_position-256:in_gene_position+257]"
2090 |       ],
2091 |       "metadata": {
2092 |         "id": "jHZW-AwDnmde"
2093 |       },
2094 |       "execution_count": null,
2095 |       "outputs": []
2096 |     },
2097 |     {
2098 |       "cell_type": "code",
2099 |       "source": [
2100 |         "len(dna_snippet)"
2101 |       ],
2102 |       "metadata": {
2103 |         "colab": {
2104 |           "base_uri": "https://localhost:8080/"
2105 |         },
2106 |         "id": "xd-2KX6Lnxex",
2107 |         "outputId": "7de526b8-8d46-4224-d6d4-4f5126bb8605"
2108 |       },
2109 |       "execution_count": null,
2110 |       "outputs": [
2111 |         {
2112 |           "output_type": "execute_result",
2113 |           "data": {
2114 |             "text/plain": [
2115 |               "513"
2116 |             ]
2117 |           },
2118 |           "metadata": {},
2119 |           "execution_count": 70
2120 |         }
2121 |       ]
2122 |     },
2123 |     {
2124 |       "cell_type": "code",
2125 |       "source": [
2126 |         "dna_snippet[len(dna_snippet) // 2]"
2127 |       ],
2128 |       "metadata": {
2129 |         "colab": {
2130 |           "base_uri": "https://localhost:8080/",
2131 |           "height": 35
2132 |         },
2133 |         "id": "gjw2pKF5n3NB",
2134 |         "outputId": "608e475f-7b65-4538-883b-be29a3ea707f"
2135 |       },
2136 |       "execution_count": null,
2137 |       "outputs": [
2138 |         {
2139 |           "output_type": "execute_result",
2140 |           "data": {
2141 |             "text/plain": [
2142 |               "'G'"
2143 |             ],
2144 |             "application/vnd.google.colaboratory.intrinsic+json": {
2145 |               "type": "string"
2146 |             }
2147 |           },
2148 |           "metadata": {},
2149 |           "execution_count": 74
2150 |         }
2151 |       ]
2152 |     },
2153 |     {
2154 |       "cell_type": "code",
2155 |       "source": [
2156 |         "DefaultDict(lambda key: key + 5)"
2157 |       ],
2158 |       "metadata": {
2159 |         "id": "gAo7w-Y33V8O"
2160 |       },
2161 |       "execution_count": null,
2162 |       "outputs": []
2163 |     },
2164 |     {
2165 |       "cell_type": "code",
2166 |       "source": [
2167 |         "foo = \"AAATAAA\"\n",
2168 |         "\n",
2169 |         "foo[len(foo) // 2]"
2170 |       ],
2171 |       "metadata": {
2172 |         "colab": {
2173 |           "base_uri": "https://localhost:8080/",
2174 |           "height": 35
2175 |         },
2176 |         "id": "vHV2Isu9oGDd",
2177 |         "outputId": "238229fc-37ab-42a0-e54a-085b756d7db6"
2178 |       },
2179 |       "execution_count": null,
2180 |       "outputs": [
2181 |         {
2182 |           "output_type": "execute_result",
2183 |           "data": {
2184 |             "text/plain": [
2185 |               "'T'"
2186 |             ],
2187 |             "application/vnd.google.colaboratory.intrinsic+json": {
2188 |               "type": "string"
2189 |             }
2190 |           },
2191 |           "metadata": {},
2192 |           "execution_count": 76
2193 |         }
2194 |       ]
2195 |     },
2196 |     {
2197 |       "cell_type": "code",
2198 |       "source": [
2199 |         "foo[3-10:3+2]"
2200 |       ],
2201 |       "metadata": {
2202 |         "colab": {
2203 |           "base_uri": "https://localhost:8080/",
2204 |           "height": 35
2205 |         },
2206 |         "id": "JDgLsIEpoOoZ",
2207 |         "outputId": "f8fc1f3c-a984-48dc-c192-73d88787430b"
2208 |       },
2209 |       "execution_count": null,
2210 |       "outputs": [
2211 |         {
2212 |           "output_type": "execute_result",
2213 |           "data": {
2214 |             "text/plain": [
2215 |               "'AAATA'"
2216 |             ],
2217 |             "application/vnd.google.colaboratory.intrinsic+json": {
2218 |               "type": "string"
2219 |             }
2220 |           },
2221 |           "metadata": {},
2222 |           "execution_count": 115
2223 |         }
2224 |       ]
2225 |     }
2226 |   ]
2227 | }


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