Data_Generation_and_Insertion.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'synthetic_data.fast'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio.Seq import Seq\n",
    "from Bio.SeqRecord import SeqRecord\n",
    "from Bio import SeqIO\n",
    "import random\n",
    "\n",
    "def generate_random_dna(length):\n",
    "    return ''.join(random.choices('ACGT', k=length))\n",
    "\n",
    "def create_fast_file(filename, num_sequences, length):\n",
    "    records = []\n",
    "    for i in range(num_sequences):\n",
    "        seq = generate_random_dna(length)\n",
    "        record = SeqRecord(Seq(seq), id=f\"seq{i}\", description=\"\")\n",
    "        records.append(record)\n",
    "    SeqIO.write(records, filename, \"fasta\")\n",
    "    return filename\n",
    "\n",
    "# Run the function in a cell\n",
    "filename = create_fast_file(\"synthetic_data.fast\", 100, 1000)\n",
    "filename  # Display the generated file name\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('seq0',\n",
       "  'CAATCGTAAATAGCTCCCGTTGTGTATAAGGGTGCAGCACCGGATGCTAATAGCGTAGGACAAAAACTACAATAAGTTTGAAAATAGAACGCCTGACTACCGGCACATCCTCGCTTTGCTGCCGGCCGTTACCGCGAGTTCTAATGGGTCAACTCTATAGGGCGACCGTCGAGGTGAATGTCCTGAGCAGCGTGAACCACTTAACATCAATAATAGGGGCCCGTTAGATTAATGCTGGTGATGCTGCTCAGATGGCTGTTAGGCCCATACCAAGTGGAGACCGGTTCCCCGTACTGTCGAGTAGCGTCGCTACGCCCAATTTGCAAGCAAGCACCACAATGGAGCCAGAAAGGTGCGGAGCTGCTCGCCAGCGCGGCGTGAGGTGAAGCCCCGTAGGAATACGACCTTTGGGAAAACGGGCAAACTATTGCACTGGGTCGGGTCCTGACGTTACATTTCTGACGCCAGCCAATCAAGAACTGGCACCAGCATGGAAAGTTGACCAATAGCGGCCCTCACTACAATTTCTTGCGGTCTGGCTGACGAAACGTATCCGGTTTAATCGAGGCAAAGGATGTGTTGATCTCCGTTGTGGCTTATTCCTATATAGAATACATGCGGTCCTTGCAGCGTATTTCAATTATATTGTCGGACAATTTTGCTCCACGCGATGTTCTTAAGTATTATGATTGAAGGTCATGAAGGATCGGTCGGTTCGCGTAAAGGGGACAACAATCTATGCGCGACTATCTGACCCGAGGGGAACCGAACATGGAGCGCGAGCGTCAGCAAGTATGCCGCATCTCGCTACATTCGAACGCGCTACACGTGGCAGCTTTTATCTGCACATATAATACTTTAACCCGCACAGATTGATCTTTTTACACTAACACAAATCGGTCGGCGAATTTGTGGCTTAGTAGAGTAGTGCGTGGTTGGACCTCGAGTGGCTACTGCTATATTGCTAGGAGTACGACTACTGCCTGCCGTTACACTCCCG'),\n",
       " ('seq1',\n",
       "  'TTTTTATTGGCGGTGTGTCCGACAACCGATAGCATGCAACCTAGTGTCATCTTGATGCCGGTAGAGGCTCGTAAGACTGGCCCACTCATTTGGGTATGTGCCCTGGCTTGGGTTGGCTCGGGGAGTAATCACGTGTACACGTTAGTCTCGCAGCGTATGGCTGTCACCGAACACGGGCCATTACAGGCAGACTAAAGCGAGTCTATTGATAGGCGAAAGACCTATCTGACCGCAGTCCCCGTGCAGTTGTTCATCTTAAGCCAGACGAGTCGGGAAAATTCCATTTTCAGCTCTTATATAACTAAGATGAAAACTACCGAACTGTATGAGGCAAGAACCTCCAGTGAGTTGTATTTGCGGACTGCCGCGACATATTGGACCAGTGTTAGAAAGGACTAGCCGGTTGGTTCGCATCGTCGTATGCCGGGAGTAGGCTCCGTGTGATAGACGGATCGCCTTAGAATTTCTCGAATGATCTTATGAACGAATCGAGACTACAGGCCGGACCTTTTACCGCTCCCTAGCGGAGTCCTCGAAGGCTATTGGAGCAGAGACGGTGCCAGCGCAGGCGCGCCACATCATGGGCCGACGGCCTGCATCTAATTGTGTGATCGGAGGGCTCGTACATGGGCCTTCCGGCTTATTAACGGTGTTGACCTTCAGGTTTGGATAAAGGTCAACATACTCAGCCAATACCGTCACGAAGACCAGAGGGTAGGTTTAGGAAAGTGTGCTAAATTGAAAACAGGTTGAGAGCGACAGGTTATCTCGCGAATCTCCATCACATCCAGGAAGACCGACCATATATCACCAGCACATTAGACCACCTTGTAGAGCGTAAAGTTGATCGCGACTCCCACTACGTGTTAAGAGAGTAGTTGCTGCACAGTCATCGGAGTTAGCTGTCCGCGATAACGAATACTGGTGAGAGCAGACATCAGACGAACGAACCCGAACGTGCACAAACAGCGTGATGGTTCTGGCGTCCGCCACCTCGGGG'),\n",
       " ('seq2',\n",
       "  'GAACTATGTTGTCAACCAGACGTTCAGTCCCTATAGCTGACTCCGGATCTCGTGCTGCCCGATCAAAAAGGCCGAAAAATGACGACGCCTTAGCGCCAATACTCAGTGTCCCTAACAGCCCACAACGTTTGGGGCACCATACATCCCTTCACGTAGGCGTCCTATGGGGTCGCAAAATTTCGATACATAGCAAAAATCATCTGATCTACGGTGGAAAAACTCCGGGACTAATAACAGCGGTGGTAATGCTCTTATGAACCAAAGGTTACGGAAATCAGAGGCTCTTTAAAGCAATAACCAGGAGCCCGTGGTTACACACATGGGCACTCTCCGAACTCGCCGATACGGTGCGCCGTTTGTCTGGTTGATCTCTTGGTGGAAAACGTCATACGACACAACCGCAGCGGGGTCCCGACATGGTCGCGGCCCGTAAGCTACCTTGCCCGTCAGGCTGCTACAATTATGCACTGCAACTCCCGTACACCCGTAGTCCTAGCGCTTTAACACCAGCTTGGTCTCATCCTATTCGGCCTTTCATTCCGATTGCGCGCCCGTTGAAGTTCTTAATGTGTTAGGGATAGACGAGGTTGGGCTAAATATCGCGACATGGATAGATGACTCGAAGCCAAGCTGAGCAAGAGCAATCTGTTAACCCTACTGCGCACTCTCTGATACTCTATCGCCCAAAGGACACAACGTCCGAACGTGGTCCCACCTCCGATTTATGGCCAGACTCATCACCTACAGTGTTCTTCATATGAGGGACACGAGGCCAACGGTGACATGGCACGGTAGTTGGAAGGCGTCAAAATGACAGGTCACAGAAGCGGGAAAACCTATACTTACATTACTAATGGGCGCCGAAGCCCGGACTCCTACTGATCTGCTCGGCGGGCACCGTAACGTCTCATTGCCTGCATTCCAACGGGATAAAAAACCGAATGTCAGAGTAGATCTGCCATGACAAATACGGCGCCTCATATACGAGGTATAGTCGGAG'),\n",
       " ('seq3',\n",
       "  'CATATTGTCCGGTCTCGCAGTATCCTCCAGAGATGCTTCGAGTGCCTGGCAGCACCCACGGAGGCCGCATTTGGTGACTTTTTTATGTACGTCGGTTAAAACGCGAGAAAGTCACCAGGGCGATCCCTAGTCTGACTGTTAGAAACGTCACAACCACCACTTATGTACGACATTAGTGGAAGACCAGTCCTTTTCCGCTGTCTATTACGCCGTGATAACCAGGATTGGGCTGCTTGCCGCCTAGTCCATCAAGGTCATCCCTAGTTTCCTGTGAATAATGGCGGGTGAATACTTGGCTCGCAGCCAAATCAAATCTTTCTTATTCCACACGAGATGAACAAGCACTACCTCAGGGCACGCTGCGCCGCGGACCGAAGTCGATCCTCATTAATGATCGGGTGAAAGGGCGAGTCATTCATGCAGCGAATCGCGTAGCTCATTTGAAATGCACCCACTACCACTGGTGCAGAAGCCGGCCGAAGGGGTCCTTGCGTCCAGTTCGTGCACATGGTAGGGCCCCCCAGACGCATCGAACGAGGATAGCAGATCTCAGTGTCGTACCAGCGTGTATGCATGTTGAACCATGACGGTGAGAAACCTGGGCCAAGTCCCGGGGAGAGCGCGTGATTTCGCGAAGCCCGGTTCTTATAGTGCGTTGTCATGGACTTAATGGACCTGGCGGTTACTCACTCGATATTTTCCCATTTTTTCGGCTTCCAGGCCGTACAGAAGTATTGACCGGTGCTGCATATCAGATAACAAATAACCAGGTTGGGATGACTTGGTCATAGAGGCTAAGGGTGGGCACTCTTTCTCTATGTCTACGCAGCAGACATACCCGTTAGGTAGAGATGCCGGCGCTTGTTTCCATGAAGGTTCGTAGAAATACATCAGGCTATCAATAGGTTATCAGCTTATCGCGGTCGTTCTTGATCAGGGTGGCTCTAATCCAGGTCCTCTGGGAGTTAGTTGGACTTTCAGACTTACGGGGGAAAAAGAC'),\n",
       " ('seq4',\n",
       "  'GGAAATCATTGCTAACTGCATGTTCGCAAAACACTAGGCTGGTTCTGGGTCCCGAGTATCGCCTCACTAAAATCCCTAGGTTGGCAAAAGCCTTACCGGGTGAAGCACCGTCGGTCGCTCGGCGGAATCACGGGTTGTCATGGGTCGTCTGGGCCCTCAAGCTTCCAAAGCGCCCACCACCTTGCGTACAGAGACGATGGCACCTCCCGGCACTATGTAGTCTAGTTGGCGGCCCATAAGTACGATGAGGGCCCCTATTGACACCAGATAACTGACTTGTCGGGTGTTGGAATCCGATCTCAAATCTTCCCATTAAGACTCTGATACTGAGGGCCCCCCCCCCACCTGCTTCCGGAGGCAGGTGTGTGATCCTGTGGCACGGCCGCACTGTTTTGTAGTTTGATTACGTTGGGGAGGGCTATCACTCACGCCGACTATTGCTCGACAAATTCGCGCTAAAAAACGATTATCTTGTAGTTTTGACGATGGCCGTTTCCACTGTCACCTCTTACCTTCCTAACTAAGGAAATGTGCTTGGCAATGGGTAAGTACGTGTCCGAGATGCGGCGCTATACGACGGAATAAACCCCTATGTTAGCTATTGCGGAACACGCCCGCCGGTAGTCATTTCGTAATGTAGGAAAATGCAACTTTGAGAACGTGGATCCCGTCTGTAACTTGATGATCAATATTTTTTCGATACAAAACTAAGCGTAAGGACCGATCTTGTTACGGGTGACCTCAGCTCATAATTCCCGACGAAAGTAAATCTATTCCACGTGGCCATGACGCCACATCCAATCGAATACTTTCATCCGATTGCTGCGCCAGGGGGTCGTGCCCGCCGGTCCGGTAATAACTGTAAACTTAATCCATCTGGTCGGCAAAGACCTAACTCACTGCTTGATCTTCCGTCTCAGGGCGGCGACACCTGTAGAGAATCTCGTAGCATAACAGCGTCCAACTGGTCGTCTGGGCAGGGGAGAGTTTCTCCGTAAAA')]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Read and display the generated FASTA file\n",
    "def display_fasta_file(filename):\n",
    "    sequences = []\n",
    "    for record in SeqIO.parse(filename, \"fasta\"):\n",
    "        sequences.append((record.id, str(record.seq)))\n",
    "    return sequences\n",
    "\n",
    "# Display the first few sequences from the file\n",
    "sequences = display_fasta_file(filename)\n",
    "sequences[:5]  # Show the first 5 sequences"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import psycopg2\n",
    "from Bio import SeqIO\n",
    "\n",
    "conn = psycopg2.connect(\"dbname=dna user=postgres \")\n",
    "cur = conn.cursor()\n",
    "\n",
    "for record in SeqIO.parse(\"synthetic_data.fast\", \"fasta\"):\n",
    "    cur.execute(\"INSERT INTO dna_sequences (name, sequence) VALUES (%s, %s::dna);\", (record.id, str(record.seq)))\n",
    "    \n",
    "conn.commit()\n",
    "cur.close()\n",
    "conn.close()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import psycopg2\n",
    "from Bio import SeqIO\n",
    "\n",
    "conn = psycopg2.connect(\"dbname=dna user=postgres \")\n",
    "cur = conn.cursor()\n",
    "\n",
    "for record in SeqIO.parse(\"synthetic_data.fast\", \"fasta\"):\n",
    "    cur.execute(\"INSERT INTO dna_sequences (name, sequence) VALUES (%s, %s::dna);\", (record.id, str(record.seq)))\n",
    "    \n",
    "conn.commit()\n",
    "cur.close()\n",
    "conn.close()\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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