Searching with regex

regex_stuff.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "e87ebdef-05bd-426d-bc6b-ffbff8376e17",
   "metadata": {},
   "outputs": [],
   "source": [
    "import re\n",
    "import random\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4160b5f6-aaf2-4b3d-b429-e38e3ceb015c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'A\\nA  \\nA\\n\\n\\nA CA\\nAC \\nT \\nGGC\\nTAT\\nT  \\nCCAG \\nTGA AATGG\\nCT A GA\\n\\nG CTG TTTGAACC\\nAC\\nACTGA\\nT GA AATGA\\nT ATT TTC AAT\\nGGTCC C TGCGA\\n CT\\nCATGTCAA\\nGGGT \\n T C\\nCCCTT G C TGGAG T\\n CG\\n \\nTC \\n\\nCGA  CCA   AAAGT\\nTGT CGGCC \\nCC\\nT\\nCT GA\\nGACA G TGC  CGAG\\nTCC\\nTTA CC \\nCGTGG\\nACAATATGCT CG\\nGAA  TC CGCCGGG\\nGTCC\\nC\\nA CG\\nT \\nAT\\nGGACG\\n\\nGAG\\n AT  \\nGC\\nAAACACCAA TACGTCAG GC\\n AGGG\\nG\\nAT\\n\\nGGC A C\\n \\nC A CAT CCATCC\\nGGCC\\nATCC\\nTCA\\nAG C\\nCC\\nA '"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "''' Create a random string with GATC along with spaces and newlines\n",
    "\n",
    "random.choices : returns a list from a list of possible choices\n",
    "    \n",
    "_s : list\n",
    "    list of strings with random choices\n",
    "    \n",
    "s : str\n",
    "    the list _s joined with an empty string\n",
    "'''\n",
    "\n",
    "_s = random.choices('GACT\\n ', k=400)\n",
    "s = \"\".join(_s)\n",
    "s"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "bca8eb7e-0808-4862-b9d3-e34161126a8d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'AAAACAACTGGCTATTCCAGTGAAATGGCTAGAGCTGTTTGAACCACACTGATGAAATGATATTTTCAATGGTCCCTGCGACTCATGTCAAGGGTTCCCCTTGCTGGAGTCGTCCGACCAAAAGTTGTCGGCCCCTCTGAGACAGTGCCGAGTCCTTACCCGTGGACAATATGCTCGGAATCCGCCGGGGTCCCACGTATGGACGGAGATGCAAACACCAATACGTCAGGCAGGGGATGGCACCACATCCATCCGGCCATCCTCAAGCCCA'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'''\n",
    "use a regex to find all whitespace and replace with an empty string (\"\")\n",
    "\n",
    "\\s+ : matches one or more whitespace characters, e.g., \" \\n\\t \\n\" would be a match\n",
    "re.sub : (what_to_sub, what_to_sub_with, String_to_use)\n",
    "'''\n",
    "\n",
    "s2 = re.sub(r\"\\s+\", \"\", s)\n",
    "s2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "e6c1acb2-213b-44b0-b208-8f637e9dc13e",
   "metadata": {},
   "outputs": [],
   "source": [
    "matches = re.finditer(\"G[AC][GT][CA]\", s2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "352ef7cd-2743-4deb-9bd2-1c7093e88745",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "10 14 GCTA\n",
      "27 31 GCTA\n",
      "31 35 GAGC\n",
      "58 62 GATA\n",
      "77 81 GCGA\n",
      "138 142 GAGA\n",
      "172 176 GCTC\n",
      "205 209 GAGA\n"
     ]
    }
   ],
   "source": [
    "for m in matches:\n",
    "    print(m.start(), m.end(), s2[m.start():m.end()])\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "31df6f94-4d17-41f8-bd7f-aae029674069",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "maxwell",
   "language": "python",
   "name": "maxwell"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}