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   "cell_type": "markdown",
   "id": "7ef61cee-b754-40bb-9a5d-fc5af9f3afd0",
   "metadata": {},
   "source": [
    "# Recipes"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e4ec17e8-b02c-48c7-aa56-feae2c375b91",
   "metadata": {},
   "source": [
    "This page references recipes for common operations for the PyHMMER API, similarly to the `itertools` [recipes](https://docs.python.org/3/library/itertools.html#itertools-recipes) from the Python documentation."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f895db71-5408-48d7-b5f2-909e2900ea47",
   "metadata": {},
   "source": [
    "## Loading multiple HMMs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4914a6a6-7d3e-4a6d-ab7b-8cb61b8dc1ac",
   "metadata": {},
   "source": [
    "An adapter for loading several `HMMFile` objects into a single object to pass to .\n",
    "\n",
    "<div class=\"alert alert-info\">\n",
    "    \n",
    "Credits\n",
    "    \n",
    "The original implementation proposed by [Zachary Kurtz](https://github.com/zdk123) in [#24](https://github.com/althonos/pyhmmer/issues/24), which was failing when too many file-descriptors where open on some OS ([#48](https://github.com/althonos/pyhmmer/issues/24)), was updated to keep at most a single file open at a time.\n",
    "    \n",
    "</div>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "985ae6b7-2a63-4146-9b98-a34801ca162b",
   "metadata": {},
   "outputs": [],
   "source": [
    "import contextlib\n",
    "import itertools\n",
    "import os\n",
    "import typing\n",
    "\n",
    "from pyhmmer.plan7 import HMMFile, HMM\n",
    "\n",
    "class HMMFiles(typing.Iterable[HMM]):\n",
    "    def __init__(self, *files: typing.Union[str, bytes, os.PathLike]):\n",
    "        self.files = files\n",
    "    \n",
    "    def __iter__(self):\n",
    "        for file in self.files:\n",
    "            with HMMFile(file) as hmm_file:\n",
    "                yield from hmm_file"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dfcb96c9-85c1-4f8d-94a3-ddf274d959ec",
   "metadata": {},
   "source": [
    "To use it with `hmmsearch`, simply create a `HMMFiles` object with the paths for the different HMM files to concatenate. They will be read in the order given as argument."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0a0a3b40-9556-415d-8a73-ed765df33fa4",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pyhmmer\n",
    "from pyhmmer.easel import SequenceFile\n",
    "\n",
    "with SequenceFile(\"data/seqs/938293.PRJEB85.HG003687.faa\", digital=True) as sequences:\n",
    "    targets = sequences.read_block()\n",
    "\n",
    "hmm_files = HMMFiles(\"data/hmms/txt/PKSI-AT.hmm\", \"data/hmms/txt/LuxC.hmm\")\n",
    "all_hits = list(pyhmmer.hmmsearch(hmm_files, targets))\n",
    "    \n",
    "print(\"HMMs searched:\", len(all_hits))\n",
    "print(\"Hits found:   \", sum(len(hits) for hits in all_hits))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d447f43b-3a46-461d-a750-ac5725705b06",
   "metadata": {},
   "source": [
    "If your filenames are stored in a list, just use the [*splat* operator](https://docs.python.org/3/tutorial/controlflow.html#unpacking-argument-lists) to unpack it:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16f217e0-1b4c-4a54-9149-27b59c3b46dd",
   "metadata": {},
   "outputs": [],
   "source": [
    "filenames = [\"data/hmms/txt/PKSI-AT.hmm\", \"data/hmms/txt/LuxC.hmm\"]\n",
    "hmm_files = HMMFiles(*filenames)"
   ]
  }
 ],
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