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   "source": [
    "# Library: Custom Species"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "By default, `TCRconvert` supports alpha-beta and gamma-delta V, D, J, and C genes for human, mouse, and rhesus macaque from the IMGT F+ORF+in-frame P references. For other species, follow these steps:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Create a folder of IMGT FASTA files\n",
    "\n",
    "The simplest way is to download from [IMGT](https://www.imgt.org/vquest/refseqh.html).\n",
    "\n",
    "**Details:**\n",
    "\n",
    "`TCRconvert` expects a folder containing files ending in `.fasta` or `.fa` with headers in the IMGT format:\n",
    "\n",
    "```\n",
    ">SomeText|TRBV10-1*02|MoreText|...\n",
    "```\n",
    "\n",
    "The sequences are not used, so a text file containing headers and ending in `.fa` would also work."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Run `build_lookup_from_fastas()`\n",
    "\n",
    "The `species` parameter should be the species name you'll use when calling `convert_gene()`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import tcrconvert\n",
    "import os\n",
    "\n",
    "# Using our example directory of fasta files\n",
    "fastadir = tcrconvert.get_example_path('fasta_dir')\n",
    "\n",
    "# Build lookup tables and note where they're being written to\n",
    "new_lookup_dir = tcrconvert.build_lookup_from_fastas(fastadir, species='rabbit')\n",
    "new_lookup_dir"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Confirm they exist there:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "os.listdir(new_lookup_dir)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Details:**\n",
    "\n",
    "`species` will also be the name of the folder storing lookup tables, so these characters are not allowed:\n",
    "\n",
    "`` / \\ : * ? \" < > | ~ ` \\n \\t``"
   ]
  }
 ],
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