nf_notebook.ipynb

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    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
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  "cells": [
    {
      "cell_type": "markdown",
      "source": [
        "# Using Nextflow to convert TCRs\n",
        "\n",
        "This notebook converts some TCRs from 10X format to Adaptive using Nextflow and tcrconverter."
      ],
      "metadata": {
        "id": "921tcClfh0Cb"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Setup\n",
        "\n",
        "First, clone the repository with the files we need.\n",
        "\n"
      ],
      "metadata": {
        "id": "hAzyNyzdiDT5"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "! git clone https://github.com/emjbishop/nextflow-example.git"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "VDO2B6ytiJEG",
        "outputId": "7222be0f-549a-4e16-c42c-43c4fe7376d8"
      },
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Cloning into 'nextflow-example'...\n",
            "remote: Enumerating objects: 5, done.\u001b[K\n",
            "remote: Counting objects: 100% (5/5), done.\u001b[K\n",
            "remote: Compressing objects: 100% (5/5), done.\u001b[K\n",
            "remote: Total 5 (delta 0), reused 5 (delta 0), pack-reused 0\u001b[K\n",
            "Receiving objects: 100% (5/5), done.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Run the bash script that installs Nextflow and tcrconverter."
      ],
      "metadata": {
        "id": "nmuoIeQ3imY6"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "! chmod +x /content/nextflow-example/notebook_setup.sh\n",
        "! /content/nextflow-example/notebook_setup.sh"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "1cOVcIooirR9",
        "outputId": "99101a2f-8abf-46fc-9f5f-eb9531e3a682"
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      "outputs": [
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          "text": [
            "CAPSULE: Downloading dependency org.apache.groovy:groovy:jar:4.0.21\n",
            "CAPSULE: Downloading dependency org.multiverse:multiverse-core:jar:0.7.0\n",
            "CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.4.14\n",
            "CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-databind:jar:2.17.0\n",
            "CAPSULE: Downloading dependency commons-io:commons-io:jar:2.11.0\n",
            "CAPSULE: Downloading dependency com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava\n",
            "CAPSULE: Downloading dependency org.yaml:snakeyaml:jar:2.2\n",
            "CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:jar:6.6.1.202309021850-r\n",
            "CAPSULE: Downloading dependency com.beust:jcommander:jar:1.35\n",
            "CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.5.2\n",
            "CAPSULE: Downloading dependency jline:jline:jar:2.9\n",
            "CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:2.0.7\n",
            "CAPSULE: Downloading dependency com.github.zafarkhaja:java-semver:jar:0.9.0\n",
            "CAPSULE: Downloading dependency com.google.guava:guava:jar:33.0.0-jre\n",
            "CAPSULE: Downloading dependency io.nextflow:nextflow:jar:24.04.2\n",
            "CAPSULE: Downloading dependency javax.mail:mail:jar:1.4.7\n",
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            "CAPSULE: Downloading dependency org.iq80.leveldb:leveldb-api:jar:0.12\n",
            "CAPSULE: Downloading dependency org.codehaus.gpars:gpars:jar:1.2.1\n",
            "CAPSULE: Downloading dependency com.esotericsoftware.kryo:kryo:jar:2.24.0\n",
            "CAPSULE: Downloading dependency org.apache.groovy:groovy-templates:jar:4.0.21\n",
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            "CAPSULE: Downloading dependency com.googlecode.javaewah:JavaEWAH:jar:1.2.3\n",
            "CAPSULE: Downloading dependency org.apache.groovy:groovy-xml:jar:4.0.21\n",
            "CAPSULE: Downloading dependency dev.failsafe:failsafe:jar:3.1.0\n",
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            "CAPSULE: Downloading dependency org.pf4j:pf4j-update:jar:2.3.0\n",
            "CAPSULE: Downloading dependency org.pf4j:pf4j:jar:3.10.0\n",
            "CAPSULE: Downloading dependency org.apache.groovy:groovy-json:jar:4.0.21\n",
            "CAPSULE: Downloading dependency org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0\n",
            "CAPSULE: Downloading dependency commons-codec:commons-codec:jar:1.15\n",
            "CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:24.04.2\n",
            "CAPSULE: Downloading dependency org.apache.groovy:groovy-nio:jar:4.0.21\n",
            "CAPSULE: Downloading dependency org.checkerframework:checker-qual:jar:3.41.0\n",
            "CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:2.0.7\n",
            "CAPSULE: Downloading dependency com.google.code.findbugs:jsr305:jar:3.0.2\n",
            "CAPSULE: Downloading dependency commons-lang:commons-lang:jar:2.6\n",
            "CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.15.4\n",
            "CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:24.04.2\n",
            "CAPSULE: Downloading dependency org.objenesis:objenesis:jar:2.1\n",
            "CAPSULE: Downloading dependency ch.artecat.grengine:grengine:jar:3.0.2\n",
            "CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-core:jar:2.17.0\n",
            "CAPSULE: Downloading dependency org.iq80.leveldb:leveldb:jar:0.12\n",
            "CAPSULE: Downloading dependency com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:jar:2.17.0\n",
            "\n",
            "      N E X T F L O W\n",
            "      version 24.04.2 build 5914\n",
            "      created 29-05-2024 06:19 UTC \n",
            "      cite doi:10.1038/nbt.3820\n",
            "      http://nextflow.io\n",
            "\n",
            "\n",
            "Nextflow installation completed. Please note:\n",
            "- the executable file `nextflow` has been created in the folder: /content\n",
            "- you may complete the installation by moving it to a directory in your $PATH\n",
            "\n",
            "Cloning into 'tcr-converter'...\n",
            "remote: Enumerating objects: 307, done.\u001b[K\n",
            "remote: Counting objects: 100% (307/307), done.\u001b[K\n",
            "remote: Compressing objects: 100% (201/201), done.\u001b[K\n",
            "remote: Total 307 (delta 127), reused 262 (delta 85), pack-reused 0\u001b[K\n",
            "Receiving objects: 100% (307/307), 2.89 MiB | 8.31 MiB/s, done.\n",
            "Resolving deltas: 100% (127/127), done.\n",
            "Processing ./tcr-converter\n",
            "  Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from tcrconverter==0.1) (2.0.3)\n",
            "Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.10/dist-packages (from pandas->tcrconverter==0.1) (2.8.2)\n",
            "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->tcrconverter==0.1) (2023.4)\n",
            "Requirement already satisfied: tzdata>=2022.1 in /usr/local/lib/python3.10/dist-packages (from pandas->tcrconverter==0.1) (2024.1)\n",
            "Requirement already satisfied: numpy>=1.21.0 in /usr/local/lib/python3.10/dist-packages (from pandas->tcrconverter==0.1) (1.25.2)\n",
            "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.8.2->pandas->tcrconverter==0.1) (1.16.0)\n",
            "Building wheels for collected packages: tcrconverter\n",
            "  Building wheel for tcrconverter (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for tcrconverter: filename=tcrconverter-0.1-py3-none-any.whl size=31535 sha256=4ccee249bb79e9c5661dbd96a3fb08e862ea9a20adda0719e5bfe91bf1f2235e\n",
            "  Stored in directory: /root/.cache/pip/wheels/7b/96/40/93936988ba4aba8a1c11a4c60e274d38242041dcd2708ffc55\n",
            "Successfully built tcrconverter\n",
            "Installing collected packages: tcrconverter\n",
            "Successfully installed tcrconverter-0.1\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Confirm Nextflow is installed properly."
      ],
      "metadata": {
        "id": "XhlU1O34jZYR"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "! nextflow info"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "EdKhVh01jbM8",
        "outputId": "54e5a79a-37dd-4ae4-a83c-34decd4cec08"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "  Version: 24.04.2 build 5914\n",
            "  Created: 29-05-2024 06:19 UTC \n",
            "  System: Linux 6.1.85+\n",
            "  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.22+7-post-Ubuntu-0ubuntu222.04.1\n",
            "  Encoding: UTF-8 (UTF-8)\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Conversion\n",
        "\n",
        "Take a look at the input data, in 10X format."
      ],
      "metadata": {
        "id": "Cf3suiSGjs_E"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd\n",
        "\n",
        "pd.read_csv('/content/tcr-converter/tcrconverter/data/example_10x.csv')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 313
        },
        "id": "2ker-y_GijQY",
        "outputId": "3a9e8d62-e38b-4c16-f973-aa4b4c325b25"
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "              barcode  is_cell                    contig_id  high_confidence  \\\n",
              "0  AAACCTGAGACCACGA-1     True  AAACCTGAGACCACGA-1_contig_1             True   \n",
              "1  AAACCTGAGACCACGA-1     True  AAACCTGAGACCACGA-1_contig_3             True   \n",
              "2  AAACCTGAGGCTCTTA-1     True  AAACCTGAGGCTCTTA-1_contig_1             True   \n",
              "3  AAACCTGAGGCTCTTA-1     True  AAACCTGAGGCTCTTA-1_contig_2             True   \n",
              "4  AAACCTGAGTGAACGC-1     True  AAACCTGAGTGAACGC-1_contig_1             True   \n",
              "\n",
              "   length chain   v_gene d_gene   j_gene c_gene  full_length  productive  \\\n",
              "0     521   TRA  TRAV1-2    NaN   TRAJ12   TRAC         True        True   \n",
              "1     584   TRB  TRBV6-1  TRBD2  TRBJ2-1  TRBC2         True        True   \n",
              "2     551   TRB  TRBV6-4  TRBD2  TRBJ2-3  TRBC2         True        True   \n",
              "3     518   TRA  TRAV1-2    NaN   TRAJ33   TRAC         True        True   \n",
              "4     674   TRB    TRBV2  TRBD1  TRBJ1-2  TRBC1         True        True   \n",
              "\n",
              "              cdr3                                        cdr3_nt  reads  \\\n",
              "0     CAVMDSSYKLIF           TGTGCTGTGATGGATAGCAGCTATAAATTGATCTTC   1569   \n",
              "1  CASSGLAGGYNEQFF  TGTGCCAGCAGTGGACTAGCGGGGGGCTACAATGAGCAGTTCTTC   5238   \n",
              "2  CASSGVAGGTDTQYF  TGTGCCAGCAGTGGGGTAGCGGGAGGCACAGATACGCAGTATTTT   3846   \n",
              "3     CAVKDSNYQLIW           TGTGCTGTGAAGGATAGCAACTATCAGTTAATCTGG   2019   \n",
              "4    CASNQGLNYGYTF        TGTGCCAGCAATCAGGGCCTTAACTATGGCTACACCTTC   3002   \n",
              "\n",
              "   umis raw_clonotype_id         raw_consensus_id  \n",
              "0     2      clonotype16  clonotype16_consensus_1  \n",
              "1     7      clonotype16  clonotype16_consensus_2  \n",
              "2     4      clonotype26  clonotype26_consensus_2  \n",
              "3     2      clonotype26  clonotype26_consensus_1  \n",
              "4     6      clonotype81  clonotype81_consensus_2  "
            ],
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              "\n",
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              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>barcode</th>\n",
              "      <th>is_cell</th>\n",
              "      <th>contig_id</th>\n",
              "      <th>high_confidence</th>\n",
              "      <th>length</th>\n",
              "      <th>chain</th>\n",
              "      <th>v_gene</th>\n",
              "      <th>d_gene</th>\n",
              "      <th>j_gene</th>\n",
              "      <th>c_gene</th>\n",
              "      <th>full_length</th>\n",
              "      <th>productive</th>\n",
              "      <th>cdr3</th>\n",
              "      <th>cdr3_nt</th>\n",
              "      <th>reads</th>\n",
              "      <th>umis</th>\n",
              "      <th>raw_clonotype_id</th>\n",
              "      <th>raw_consensus_id</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>AAACCTGAGACCACGA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGACCACGA-1_contig_1</td>\n",
              "      <td>True</td>\n",
              "      <td>521</td>\n",
              "      <td>TRA</td>\n",
              "      <td>TRAV1-2</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TRAJ12</td>\n",
              "      <td>TRAC</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CAVMDSSYKLIF</td>\n",
              "      <td>TGTGCTGTGATGGATAGCAGCTATAAATTGATCTTC</td>\n",
              "      <td>1569</td>\n",
              "      <td>2</td>\n",
              "      <td>clonotype16</td>\n",
              "      <td>clonotype16_consensus_1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>AAACCTGAGACCACGA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGACCACGA-1_contig_3</td>\n",
              "      <td>True</td>\n",
              "      <td>584</td>\n",
              "      <td>TRB</td>\n",
              "      <td>TRBV6-1</td>\n",
              "      <td>TRBD2</td>\n",
              "      <td>TRBJ2-1</td>\n",
              "      <td>TRBC2</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CASSGLAGGYNEQFF</td>\n",
              "      <td>TGTGCCAGCAGTGGACTAGCGGGGGGCTACAATGAGCAGTTCTTC</td>\n",
              "      <td>5238</td>\n",
              "      <td>7</td>\n",
              "      <td>clonotype16</td>\n",
              "      <td>clonotype16_consensus_2</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>AAACCTGAGGCTCTTA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGGCTCTTA-1_contig_1</td>\n",
              "      <td>True</td>\n",
              "      <td>551</td>\n",
              "      <td>TRB</td>\n",
              "      <td>TRBV6-4</td>\n",
              "      <td>TRBD2</td>\n",
              "      <td>TRBJ2-3</td>\n",
              "      <td>TRBC2</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CASSGVAGGTDTQYF</td>\n",
              "      <td>TGTGCCAGCAGTGGGGTAGCGGGAGGCACAGATACGCAGTATTTT</td>\n",
              "      <td>3846</td>\n",
              "      <td>4</td>\n",
              "      <td>clonotype26</td>\n",
              "      <td>clonotype26_consensus_2</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>AAACCTGAGGCTCTTA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGGCTCTTA-1_contig_2</td>\n",
              "      <td>True</td>\n",
              "      <td>518</td>\n",
              "      <td>TRA</td>\n",
              "      <td>TRAV1-2</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TRAJ33</td>\n",
              "      <td>TRAC</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CAVKDSNYQLIW</td>\n",
              "      <td>TGTGCTGTGAAGGATAGCAACTATCAGTTAATCTGG</td>\n",
              "      <td>2019</td>\n",
              "      <td>2</td>\n",
              "      <td>clonotype26</td>\n",
              "      <td>clonotype26_consensus_1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>AAACCTGAGTGAACGC-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGTGAACGC-1_contig_1</td>\n",
              "      <td>True</td>\n",
              "      <td>674</td>\n",
              "      <td>TRB</td>\n",
              "      <td>TRBV2</td>\n",
              "      <td>TRBD1</td>\n",
              "      <td>TRBJ1-2</td>\n",
              "      <td>TRBC1</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CASNQGLNYGYTF</td>\n",
              "      <td>TGTGCCAGCAATCAGGGCCTTAACTATGGCTACACCTTC</td>\n",
              "      <td>3002</td>\n",
              "      <td>6</td>\n",
              "      <td>clonotype81</td>\n",
              "      <td>clonotype81_consensus_2</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
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            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "summary": "{\n  \"name\": \"pd\",\n  \"rows\": 5,\n  \"fields\": [\n    {\n      \"column\": \"barcode\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"AAACCTGAGACCACGA-1\",\n          \"AAACCTGAGGCTCTTA-1\",\n          \"AAACCTGAGTGAACGC-1\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"is_cell\",\n      \"properties\": {\n        \"dtype\": \"boolean\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          true\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"contig_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"AAACCTGAGACCACGA-1_contig_3\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"high_confidence\",\n      \"properties\": {\n        \"dtype\": \"boolean\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          true\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"length\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 64,\n        \"min\": 518,\n        \"max\": 674,\n        \"num_unique_values\": 5,\n        \"samples\": [\n          584\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"chain\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 2,\n        \"samples\": [\n          \"TRB\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"v_gene\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 4,\n        \"samples\": [\n          \"TRBV6-1\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"d_gene\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 2,\n        \"samples\": [\n          \"TRBD1\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"j_gene\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"TRBJ2-1\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"c_gene\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"TRAC\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"full_length\",\n      \"properties\": {\n        \"dtype\": \"boolean\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          true\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"productive\",\n      \"properties\": {\n        \"dtype\": \"boolean\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          true\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"cdr3\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"CASSGLAGGYNEQFF\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"cdr3_nt\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"TGTGCCAGCAGTGGACTAGCGGGGGGCTACAATGAGCAGTTCTTC\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"reads\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 1470,\n        \"min\": 1569,\n        \"max\": 5238,\n        \"num_unique_values\": 5,\n        \"samples\": [\n          5238\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"umis\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 2,\n        \"min\": 2,\n        \"max\": 7,\n        \"num_unique_values\": 4,\n        \"samples\": [\n          7\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"raw_clonotype_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"clonotype16\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"raw_consensus_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"clonotype16_consensus_2\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 4
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Use the Nextflow pipeline to convert to Adaptive.\n",
        "\n",
        "Note that the input and output formats have already been written into the pipeline."
      ],
      "metadata": {
        "id": "NqxN4kInjz27"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "! nextflow run nextflow-example/tcrconverter.nf \\\n",
        "  --input '/content/tcr-converter/tcrconverter/data/example_10x.csv' \\\n",
        "  --output \"example_out2.csv\""
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "102S_5EiijS9",
        "outputId": "58ec7d5b-5e16-48c6-d912-cb32b77a4e13"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\n",
            "\u001b[1m\u001b[38;5;232m\u001b[48;5;43m N E X T F L O W \u001b[0;2m  ~  \u001b[mversion 24.04.2\u001b[m\n",
            "\u001b[K\n",
            "Launching\u001b[35m `nextflow-example/tcrconverter.nf` \u001b[0;2m[\u001b[0;1;36mdeadly_poitras\u001b[0;2m] DSL2 - \u001b[36mrevision: \u001b[0;36m96e2907007\u001b[m\n",
            "\u001b[K\n",
            "TCR input: /content/tcr-converter/tcrconverter/data/example_10x.csv\n",
            "TCR output directory: /content\n",
            "\u001b[2m[\u001b[0;34m-        \u001b[0;2m] \u001b[0;2m\u001b[mconvertTCR -\u001b[K\n",
            "\u001b[2A\n",
            "\u001b[2mexecutor >  local (1)\u001b[m\u001b[K\n",
            "\u001b[2m[\u001b[0;34md2/9c714c\u001b[0;2m] \u001b[0;2m\u001b[mconvertTCR\u001b[2m |\u001b[m 0 of 1\u001b[K\n",
            "\u001b[3A\n",
            "\u001b[2mexecutor >  local (1)\u001b[m\u001b[K\n",
            "\u001b[2m[\u001b[0;34md2/9c714c\u001b[0;2m] \u001b[0;2m\u001b[mconvertTCR\u001b[2m |\u001b[m 0 of 1\u001b[K\n",
            "\u001b[3A\n",
            "\u001b[2mexecutor >  local (1)\u001b[m\u001b[K\n",
            "\u001b[2m[\u001b[0;34md2/9c714c\u001b[0;2m] \u001b[0;2m\u001b[mconvertTCR\u001b[2m |\u001b[m 1 of 1\u001b[32m ✔\u001b[m\u001b[K\n",
            "\u001b[3A\n",
            "\u001b[2mexecutor >  local (1)\u001b[m\u001b[K\n",
            "\u001b[2m[\u001b[0;34md2/9c714c\u001b[0;2m] \u001b[0;2m\u001b[mconvertTCR\u001b[2m |\u001b[m 1 of 1\u001b[32m ✔\u001b[m\u001b[K\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Now look at the output."
      ],
      "metadata": {
        "id": "7UOBNebvkI1X"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "pd.read_csv('example_out.csv')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 313
        },
        "id": "xrSTUtlPijVU",
        "outputId": "1e3aed2b-2030-496c-dc10-4a145eeb872c"
      },
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "              barcode  is_cell                    contig_id  high_confidence  \\\n",
              "0  AAACCTGAGACCACGA-1     True  AAACCTGAGACCACGA-1_contig_1             True   \n",
              "1  AAACCTGAGACCACGA-1     True  AAACCTGAGACCACGA-1_contig_3             True   \n",
              "2  AAACCTGAGGCTCTTA-1     True  AAACCTGAGGCTCTTA-1_contig_1             True   \n",
              "3  AAACCTGAGGCTCTTA-1     True  AAACCTGAGGCTCTTA-1_contig_2             True   \n",
              "4  AAACCTGAGTGAACGC-1     True  AAACCTGAGTGAACGC-1_contig_1             True   \n",
              "\n",
              "   length chain         v_gene d_gene         j_gene c_gene  full_length  \\\n",
              "0     521   TRA  TCRAV01-02*01    NaN     TCRAJ12*01   TRAC         True   \n",
              "1     584   TRB  TCRBV06-01*01  TRBD2  TCRBJ02-01*01  TRBC2         True   \n",
              "2     551   TRB  TCRBV06-04*01  TRBD2  TCRBJ02-03*01  TRBC2         True   \n",
              "3     518   TRA  TCRAV01-02*01    NaN     TCRAJ33*01   TRAC         True   \n",
              "4     674   TRB     TCRBV02*01  TRBD1  TCRBJ01-02*01  TRBC1         True   \n",
              "\n",
              "   productive             cdr3                                        cdr3_nt  \\\n",
              "0        True     CAVMDSSYKLIF           TGTGCTGTGATGGATAGCAGCTATAAATTGATCTTC   \n",
              "1        True  CASSGLAGGYNEQFF  TGTGCCAGCAGTGGACTAGCGGGGGGCTACAATGAGCAGTTCTTC   \n",
              "2        True  CASSGVAGGTDTQYF  TGTGCCAGCAGTGGGGTAGCGGGAGGCACAGATACGCAGTATTTT   \n",
              "3        True     CAVKDSNYQLIW           TGTGCTGTGAAGGATAGCAACTATCAGTTAATCTGG   \n",
              "4        True    CASNQGLNYGYTF        TGTGCCAGCAATCAGGGCCTTAACTATGGCTACACCTTC   \n",
              "\n",
              "   reads  umis raw_clonotype_id         raw_consensus_id  \n",
              "0   1569     2      clonotype16  clonotype16_consensus_1  \n",
              "1   5238     7      clonotype16  clonotype16_consensus_2  \n",
              "2   3846     4      clonotype26  clonotype26_consensus_2  \n",
              "3   2019     2      clonotype26  clonotype26_consensus_1  \n",
              "4   3002     6      clonotype81  clonotype81_consensus_2  "
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-224dea21-01aa-4b51-b50f-b5d7e193c877\" class=\"colab-df-container\">\n",
              "    <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>barcode</th>\n",
              "      <th>is_cell</th>\n",
              "      <th>contig_id</th>\n",
              "      <th>high_confidence</th>\n",
              "      <th>length</th>\n",
              "      <th>chain</th>\n",
              "      <th>v_gene</th>\n",
              "      <th>d_gene</th>\n",
              "      <th>j_gene</th>\n",
              "      <th>c_gene</th>\n",
              "      <th>full_length</th>\n",
              "      <th>productive</th>\n",
              "      <th>cdr3</th>\n",
              "      <th>cdr3_nt</th>\n",
              "      <th>reads</th>\n",
              "      <th>umis</th>\n",
              "      <th>raw_clonotype_id</th>\n",
              "      <th>raw_consensus_id</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>AAACCTGAGACCACGA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGACCACGA-1_contig_1</td>\n",
              "      <td>True</td>\n",
              "      <td>521</td>\n",
              "      <td>TRA</td>\n",
              "      <td>TCRAV01-02*01</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TCRAJ12*01</td>\n",
              "      <td>TRAC</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CAVMDSSYKLIF</td>\n",
              "      <td>TGTGCTGTGATGGATAGCAGCTATAAATTGATCTTC</td>\n",
              "      <td>1569</td>\n",
              "      <td>2</td>\n",
              "      <td>clonotype16</td>\n",
              "      <td>clonotype16_consensus_1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>AAACCTGAGACCACGA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGACCACGA-1_contig_3</td>\n",
              "      <td>True</td>\n",
              "      <td>584</td>\n",
              "      <td>TRB</td>\n",
              "      <td>TCRBV06-01*01</td>\n",
              "      <td>TRBD2</td>\n",
              "      <td>TCRBJ02-01*01</td>\n",
              "      <td>TRBC2</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CASSGLAGGYNEQFF</td>\n",
              "      <td>TGTGCCAGCAGTGGACTAGCGGGGGGCTACAATGAGCAGTTCTTC</td>\n",
              "      <td>5238</td>\n",
              "      <td>7</td>\n",
              "      <td>clonotype16</td>\n",
              "      <td>clonotype16_consensus_2</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>AAACCTGAGGCTCTTA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGGCTCTTA-1_contig_1</td>\n",
              "      <td>True</td>\n",
              "      <td>551</td>\n",
              "      <td>TRB</td>\n",
              "      <td>TCRBV06-04*01</td>\n",
              "      <td>TRBD2</td>\n",
              "      <td>TCRBJ02-03*01</td>\n",
              "      <td>TRBC2</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CASSGVAGGTDTQYF</td>\n",
              "      <td>TGTGCCAGCAGTGGGGTAGCGGGAGGCACAGATACGCAGTATTTT</td>\n",
              "      <td>3846</td>\n",
              "      <td>4</td>\n",
              "      <td>clonotype26</td>\n",
              "      <td>clonotype26_consensus_2</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>AAACCTGAGGCTCTTA-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGGCTCTTA-1_contig_2</td>\n",
              "      <td>True</td>\n",
              "      <td>518</td>\n",
              "      <td>TRA</td>\n",
              "      <td>TCRAV01-02*01</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TCRAJ33*01</td>\n",
              "      <td>TRAC</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CAVKDSNYQLIW</td>\n",
              "      <td>TGTGCTGTGAAGGATAGCAACTATCAGTTAATCTGG</td>\n",
              "      <td>2019</td>\n",
              "      <td>2</td>\n",
              "      <td>clonotype26</td>\n",
              "      <td>clonotype26_consensus_1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>AAACCTGAGTGAACGC-1</td>\n",
              "      <td>True</td>\n",
              "      <td>AAACCTGAGTGAACGC-1_contig_1</td>\n",
              "      <td>True</td>\n",
              "      <td>674</td>\n",
              "      <td>TRB</td>\n",
              "      <td>TCRBV02*01</td>\n",
              "      <td>TRBD1</td>\n",
              "      <td>TCRBJ01-02*01</td>\n",
              "      <td>TRBC1</td>\n",
              "      <td>True</td>\n",
              "      <td>True</td>\n",
              "      <td>CASNQGLNYGYTF</td>\n",
              "      <td>TGTGCCAGCAATCAGGGCCTTAACTATGGCTACACCTTC</td>\n",
              "      <td>3002</td>\n",
              "      <td>6</td>\n",
              "      <td>clonotype81</td>\n",
              "      <td>clonotype81_consensus_2</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "    <div class=\"colab-df-buttons\">\n",
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              "      display:flex;\n",
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              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
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              "      border-radius: 50%;\n",
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              "\n",
              "    .colab-df-convert:hover {\n",
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              "    .colab-df-buttons div {\n",
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              "        const docLinkHtml = 'Like what you see? Visit the ' +\n",
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              "  .colab-df-quickchart {\n",
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              "  }\n",
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              "  .colab-df-quickchart:hover {\n",
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              "  .colab-df-quickchart-complete:disabled,\n",
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              "    background-color: var(--disabled-bg-color);\n",
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              "    animation:\n",
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              "  @keyframes spin {\n",
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              "      border-bottom-color: var(--fill-color);\n",
              "      border-left-color: var(--fill-color);\n",
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              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
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              "      border-color: transparent;\n",
              "      border-right-color: var(--fill-color);\n",
              "      border-bottom-color: var(--fill-color);\n",
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              "    }\n",
              "  }\n",
              "</style>\n",
              "\n",
              "  <script>\n",
              "    async function quickchart(key) {\n",
              "      const quickchartButtonEl =\n",
              "        document.querySelector('#' + key + ' button');\n",
              "      quickchartButtonEl.disabled = true;  // To prevent multiple clicks.\n",
              "      quickchartButtonEl.classList.add('colab-df-spinner');\n",
              "      try {\n",
              "        const charts = await google.colab.kernel.invokeFunction(\n",
              "            'suggestCharts', [key], {});\n",
              "      } catch (error) {\n",
              "        console.error('Error during call to suggestCharts:', error);\n",
              "      }\n",
              "      quickchartButtonEl.classList.remove('colab-df-spinner');\n",
              "      quickchartButtonEl.classList.add('colab-df-quickchart-complete');\n",
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              "    (() => {\n",
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              "      quickchartButtonEl.style.display =\n",
              "        google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
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              "\n",
              "    </div>\n",
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            ],
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "dataframe",
              "summary": "{\n  \"name\": \"pd\",\n  \"rows\": 5,\n  \"fields\": [\n    {\n      \"column\": \"barcode\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"AAACCTGAGACCACGA-1\",\n          \"AAACCTGAGGCTCTTA-1\",\n          \"AAACCTGAGTGAACGC-1\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"is_cell\",\n      \"properties\": {\n        \"dtype\": \"boolean\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          true\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"contig_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"AAACCTGAGACCACGA-1_contig_3\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"high_confidence\",\n      \"properties\": {\n        \"dtype\": \"boolean\",\n        \"num_unique_values\": 1,\n        \"samples\": [\n          true\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"length\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 64,\n        \"min\": 518,\n        \"max\": 674,\n        \"num_unique_values\": 5,\n        \"samples\": [\n          584\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"chain\",\n      \"properties\": {\n        \"dtype\": \"category\",\n        \"num_unique_values\": 2,\n        \"samples\": [\n          \"TRB\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"v_gene\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 4,\n  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\"TGTGCCAGCAGTGGACTAGCGGGGGGCTACAATGAGCAGTTCTTC\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"reads\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 1470,\n        \"min\": 1569,\n        \"max\": 5238,\n        \"num_unique_values\": 5,\n        \"samples\": [\n          5238\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"umis\",\n      \"properties\": {\n        \"dtype\": \"number\",\n        \"std\": 2,\n        \"min\": 2,\n        \"max\": 7,\n        \"num_unique_values\": 4,\n        \"samples\": [\n          7\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"raw_clonotype_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 3,\n        \"samples\": [\n          \"clonotype16\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    },\n    {\n      \"column\": \"raw_consensus_id\",\n      \"properties\": {\n        \"dtype\": \"string\",\n        \"num_unique_values\": 5,\n        \"samples\": [\n          \"clonotype16_consensus_2\"\n        ],\n        \"semantic_type\": \"\",\n        \"description\": \"\"\n      }\n    }\n  ]\n}"
            }
          },
          "metadata": {},
          "execution_count": 7
        }
      ]
    }
  ]
}