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   "source": [
    "# Computing digests locally\n",
    "\n",
    "## Introduction\n",
    "\n",
    "This tutorial shows you how to compute GA4GH content-addressable identifiers for sequences and FASTA files using the `refget` package.\n",
    "\n",
    "<div class=\"admonition tip\">\n",
    "  <p class=\"admonition-title\">New to GA4GH digests?</p>\n",
    "  <p>See <a href=\"/refget/digests-explained/\">What are GA4GH digests?</a> for background on why content-addressable identifiers matter.</p>\n",
    "</div>\n",
    "\n",
    "<div class=\"admonition success\">\n",
    "  <p class=\"admonition-title\">Learning objectives</p>\n",
    "  <ul>\n",
    "    <li>Compute a refget sequence digest for a sequence</li>\n",
    "    <li>Compute a refget sequence collection digest from a FASTA file</li>\n",
    "    <li>Understand level 1 and level 2 representations</li>\n",
    "  </ul>\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Computing a sequence digest\n",
    "\n",
    "Use `sha512t24u_digest()` to compute the GA4GH digest for any string:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
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    "execution": {
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   "outputs": [],
   "source": [
    "from refget.digests import sha512t24u_digest\n",
    "from refget.store import digest_fasta\n",
    "from refget.utils import fasta_to_seqcol_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-01-23T03:30:31.143507Z",
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     "shell.execute_reply": "2026-01-23T03:30:31.148434Z"
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "'YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sha512t24u_digest('GGAA')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Computing a collection digest from FASTA\n",
    "\n",
    "For a FASTA file containing multiple sequences, compute the top-level collection digest:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2026-01-23T03:30:31.207271Z"
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   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "digest_fasta('../../../test_fasta/base.fa').digest"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Getting the full sequence collection (level 2)\n",
    "\n",
    "To see the complete sequence collection representation with all attributes (names, lengths, sequences, and derived attributes), use `fasta_to_seqcol_dict()`:\n",
    "\n",
    "Note: `sequences` contains `SQ.`-prefixed digests for each sequence. The `sorted_*` attributes enable order-independent comparison."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-01-23T03:30:31.208868Z",
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     "shell.execute_reply": "2026-01-23T03:30:31.211266Z"
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   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'lengths': [8, 4, 4],\n",
       " 'names': ['chrX', 'chr1', 'chr2'],\n",
       " 'sequences': ['SQ.iYtREV555dUFKg2_agSJW6suquUyPpMw',\n",
       "  'SQ.YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj',\n",
       "  'SQ.AcLxtBuKEPk_7PGE_H4dGElwZHCujwH6'],\n",
       " 'sorted_name_length_pairs': ['IWFt7HQ4XoMk34U27BKO-4szSRifP6H5',\n",
       "  'chDD8A4S8YZKNNctCimHasAA2Dn596SZ',\n",
       "  'enZNOGccwFbN9yJ3YZVifFTFCVA9hIpH'],\n",
       " 'sorted_sequences': ['SQ.iYtREV555dUFKg2_agSJW6suquUyPpMw',\n",
       "  'SQ.YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj',\n",
       "  'SQ.AcLxtBuKEPk_7PGE_H4dGElwZHCujwH6']}"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_to_seqcol_dict('../../../test_fasta/base.fa')\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Iterating over sequences\n",
    "\n",
    "For lower-level access to individual sequence metadata (name, length, digests), use the `digest_fasta` function. This returns an iterator over each sequence:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<div class=\"admonition success\">\n",
    "  <p class=\"admonition-title\">Summary</p>\n",
    "  <ul>\n",
    "    <li><code>sha512t24u_digest()</code> computes GA4GH digests for sequences</li>\n",
    "    <li><code>digest_fasta()</code> computes collection digests from FASTA files</li>\n",
    "    <li><code>fasta_to_seqcol_dict()</code> returns full level 2 sequence collection data</li>\n",
    "  </ul>\n",
    "</div>"
   ]
  }
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