kmer_generation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from Bio import SeqIO\n",
    "from collections import defaultdict\n",
    "from scipy.sparse import dok_matrix, csr_matrix\n",
    "from itertools import product\n",
    "\n",
    "def generate_kmers(sequence, k):\n",
    "    return [sequence[i:i+k] for i in range(len(sequence) - k + 1)]\n",
    "\n",
    "def count_kmers_in_seq(sequence, kmer_list):\n",
    "    kmer_counts = defaultdict(int)\n",
    "    for kmer in generate_kmers(sequence, len(next(iter(kmer_list)))):\n",
    "        if kmer in kmer_list:\n",
    "            kmer_counts[kmer] += 1\n",
    "    return kmer_counts\n",
    "\n",
    "def get_all_possible_kmers(k):\n",
    "    return {''.join(p) for p in product('ACGT', repeat=k)}\n",
    "\n",
    "def create_kmer_dataframe(fasta_file, kmer_list):\n",
    "    records = SeqIO.parse(fasta_file, \"fasta\")\n",
    "    headers = []\n",
    "    kmer_to_index = {kmer: idx for idx, kmer in enumerate(sorted(kmer_list))}\n",
    "    num_kmers = len(kmer_list)\n",
    "    num_sequences = sum(1 for _ in SeqIO.parse(fasta_file, \"fasta\"))\n",
    "    \n",
    "    data = dok_matrix((num_sequences, num_kmers), dtype=int)\n",
    "\n",
    "    for seq_idx, record in enumerate(SeqIO.parse(fasta_file, \"fasta\")):\n",
    "        headers.append(record.id)\n",
    "        sequence = str(record.seq).upper()\n",
    "        kmer_counts = count_kmers_in_seq(sequence, kmer_list)\n",
    "        for kmer, count in kmer_counts.items():\n",
    "            if kmer in kmer_to_index:\n",
    "                data[seq_idx, kmer_to_index[kmer]] = count\n",
    "\n",
    "    sparse_df = pd.DataFrame.sparse.from_spmatrix(data.tocsr(), index=headers, columns=sorted(kmer_list))\n",
    "    return sparse_df\n",
    "\n",
    "def main(promoter_fasta, non_promoter_fasta, k):\n",
    "    kmer_list = get_all_possible_kmers(k)\n",
    "    \n",
    "    promoter_df = create_kmer_dataframe(promoter_fasta, kmer_list)\n",
    "    non_promoter_df = create_kmer_dataframe(non_promoter_fasta, kmer_list)\n",
    "    \n",
    "    return promoter_df, non_promoter_df\n",
    "\n",
    "promoter_fasta = 'insert_path_to_your_promoter_fasta_file'\n",
    "non_promoter_fasta = 'insert_path_to_your_non-promoter_fasta_file'\n",
    "k = 10  # insert wanted k-length\n",
    "\n",
    "promoter_df, non_promoter_df = main(promoter_fasta, non_promoter_fasta, k)\n",
    "\n",
    "print(promoter_df)\n",
    "print(non_promoter_df)\n"
   ]
  }
 ],
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  "language_info": {
   "name": "python"
  }
 },
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