pipeline/misc/tokenization/protein-tokenization-example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ptkn import protein_tokenization, protein_tokenization_test"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Run tests\n",
    "protein_tokenization_test.ProteinTokenizationTest().test_cases()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CD4+ [term=CD4, sign=+, value=1, metadata={'name': 'CD4'}]\n",
      "CD45RA+ [term=CD45RA, sign=+, value=1, metadata={'name': 'CD45RA'}]\n",
      "CD45RO- [term=CD45RO, sign=-, value=-1, metadata={'name': 'CD45RO'}]\n",
      "4-1BB- [term=4-1BB, sign=-, value=-1, metadata={'name': '4-1BB'}]\n",
      "CD62L+++ [term=CD62L, sign=+++, value=1, metadata={'name': 'CD62L'}]\n",
      "CCR7 [term=CCR7, sign=None, value=0, metadata=None]\n",
      "CD127pos [term=CD127, sign=pos, value=1, metadata={'name': 'CD127'}]\n",
      "CD27 [term=CD27, sign=None, value=0, metadata=None]\n",
      "CD28hi [term=CD28, sign=hi, value=1, metadata={'name': 'CD28'}]\n",
      "CD95+ [term=CD95, sign=+, value=1, metadata={'name': 'CD95'}]\n",
      "TNF-α- [term=TNF-α, sign=-, value=-1, metadata={'name': 'TNF-α'}]\n",
      "CD122+ [term=CD122, sign=+, value=1, metadata={'name': 'CD122'}]\n"
     ]
    }
   ],
   "source": [
    "# Show example\n",
    "vocab_pr = [\n",
    "    'CD4', 'CD45', 'CD45RA', 'CD45RO', 'CD62L', '4-1BB', \n",
    "    'CD127', 'CD28', 'CD122', 'CD95', 'CD122', 'TNF-α'\n",
    "    # 'CCR7', 'CD27' -- intentionally omitted \n",
    "]\n",
    "vocab_pr = {k: dict(name=k) for k in vocab_pr}\n",
    "tokenizer = protein_tokenization.ProteinTokenizer(vocab_pr)\n",
    "string = 'CD4+CD45RA+CD45RO-4-1BB-CD62L+++CCR7loCD127posCD27positiveCD28hiCD95+TNF-α-CD122+'\n",
    "for t in tokenizer.tokenize(string):\n",
    "    print(f'{t.text} [term={t.token_text}, sign={t.sign_text}, value={t.sign_value}, metadata={t.metadata}]')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "589 ns ± 0.55 ns per loop (mean ± std. dev. of 7 runs, 1000000 loops each)\n"
     ]
    }
   ],
   "source": [
    "# Show benchmark\n",
    "%timeit tokenizer.tokenize(string)"
   ]
  }
 ],
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