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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Command-line: Quick Start"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Basic usage"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 1. Inspect input (optional)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!head ../../tcrconvert/examples/tenx.csv | column -t -s,"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2. Use the `convert` subcommand"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!tcrconvert convert \\\n",
    "    --input ../../tcrconvert/examples/tenx.csv \\\n",
    "    --output ../../tcrconvert/examples/converted/tenx2adapt.tsv \\\n",
    "    --frm tenx \\\n",
    "    --to adaptive"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Explanation of flags used in this command**:\n",
    "\n",
    "- `--input`/`-i`: Input file (CSV or TSV)\n",
    "\n",
    "- `--output`/`-o`: Output file (CSV or TSV)\n",
    "\n",
    "- `--frm`/`-f`: Input TCR gene format (`tenx`, `adaptive`, `adaptivev2`, or `imgt`)\n",
    "\n",
    "- `--to`/`-t`: Output TCR gene format(`tenx`, `adaptive`, `adaptivev2`, or `imgt`)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> **Tip**: Suppress INFO-level messages by setting `verbose=False`. Warnings and errors will still appear.\n",
    "\n",
    "> **Tip**: If your Adaptive data lacks `x_resolved`/`xMaxResolved` columns, create them yourself by combining the `x_gene`/`xGeneName` and `x_allele`/`xGeneAllele` columns. See the FAQs."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 3. Inspect output (optional)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!head ../../tcrconvert/examples/converted/tenx2adapt.tsv | column -t"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## AIRR data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Supply the standard AIRR gene column names individually as custom columns:\n",
    "\n",
    "- `--custom`/`-c`: Custom gene column name\n",
    "\n",
    "```bash\n",
    "$ tcrconvert convert -i airr.csv -o out.csv --frm tenx --to imgt \\\n",
    "    -c v_call \\\n",
    "    -c d_call \\\n",
    "    -c j_call \\\n",
    "    -c c_call\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Custom column names"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "By default, `TCRconvert` assumes these column names based on the input nomenclature (`--frm`/`-f`):\n",
    "\n",
    "- `--frm imgt` = `['v_gene', 'd_gene', 'j_gene', 'c_gene']`\n",
    "\n",
    "- `--frm tenx` = `['v_gene', 'd_gene', 'j_gene', 'c_gene']`\n",
    "\n",
    "- `--frm adaptive` = `['v_resolved', 'd_resolved', 'j_resolved']`\n",
    "\n",
    "- `--frm adaptivev2` = `['vMaxResolved', 'dMaxResolved', 'jMaxResolved']`\n",
    "\n",
    "You can override these columns using the `--custom`/`-c` flag:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 1. Inspect input 10X data with custom column names (optional)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!head ../../tcrconvert/examples/customcols.csv | column -t -s,"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2. Convert to IMGT, specifying columns with `--custom`/`-c`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!tcrconvert convert \\\n",
    "    -i ../../tcrconvert/examples/customcols.csv \\\n",
    "    -o ../../tcrconvert/examples/converted/custom2imgt.csv \\\n",
    "    --frm tenx \\\n",
    "    --to imgt \\\n",
    "    --verbose False \\\n",
    "    -c myVgene \\\n",
    "    -c myDgene \\\n",
    "    -c myJgene \\\n",
    "    -c myCgene"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 3. Inspect output (optional)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!head ../../tcrconvert/examples/converted/custom2imgt.csv | column -t -s,"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Rhesus or mouse data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use the `--species`/`-s` flag:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!tcrconvert convert \\\n",
    "    -i ../../tcrconvert/examples/tenx.csv \\\n",
    "    -o ../../tcrconvert/examples/converted/tenx2adapt.tsv \\\n",
    "    --frm tenx \\\n",
    "    --to adaptive \\\n",
    "    --verbose False \\\n",
    "    -s rhesus  # or mouse"
   ]
  }
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