extract_identical_headers.ipynb

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     "text": [
      "Output fasta files have been successfully created\n"
     ]
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   "source": [
    "# EXTRACTING FASTA SEQUECNES WITH IDENTICAL HEADERS HAVING DIFFERENT LENGTHS\n",
    "\n",
    "# The extracted sequences will be stored in a fasta file with an index at end of the identical headers such as\n",
    "# header_1\n",
    "# header_2 ... and so on\n",
    "\n",
    "from Bio import SeqIO\n",
    "\n",
    "# Enter the name/path of your input fasta file here\n",
    "input_fasta = \"input_fasta.fasta\"\n",
    "\n",
    "def main(input_fasta):\n",
    "    # Reading the input fasta file\n",
    "    fr = open(input_fasta,\"r\")\n",
    "    records = SeqIO.parse(fr,\"fasta\")\n",
    "    \n",
    "    # Dictionary identical_headers now store only the headers for sequences with identical headers as its keys\n",
    "    identical_headers = getting_identical_header(records)\n",
    "    fr.close()\n",
    "    \n",
    "    # Again reading our input fasta file for fetching only those sequences which have identical headers\n",
    "    fr = open(input_fasta,\"r\")\n",
    "    records = SeqIO.parse(fr,\"fasta\")\n",
    "    \n",
    "    # Dictionary identical_headers now store the complete records for sequences with identical headers\n",
    "    identical_headers = getting_identical_header_records(records, identical_headers)\n",
    "    fr.close()\n",
    "    \n",
    "    # Modifying the headers before writing to the output files (adding index to the headers)\n",
    "    identical_headers = modifying_headers(identical_headers)\n",
    "    \n",
    "    # Writing the extracted sequences with identical headers to output fasta files\n",
    "    writing_identical_header_records(identical_headers)\n",
    "    \n",
    "    print(\"Output fasta files have been successfully created\")\n",
    "\n",
    "# Function modifying_headers adds index number at the end of each identical header\n",
    "def modifying_headers(identical_headers):\n",
    "    for header in identical_headers:\n",
    "        for iteration,record in enumerate(identical_headers[header]):\n",
    "            record.description = record.description + \"_\" + str(iteration)\n",
    "    \n",
    "    return(identical_headers)\n",
    "            \n",
    "# Function writing_identical_header_records writes the fasta sequences with identical headers to output files\n",
    "def writing_identical_header_records(identical_headers):\n",
    "    for iteration,header in enumerate(identical_headers):\n",
    "        out_file_name = \"out_file_\"+str(iteration)+\".fasta\"\n",
    "        fw = open(out_file_name,\"w\")\n",
    "        SeqIO.write(identical_headers[header], fw, \"fasta\")\n",
    "        fw.close()\n",
    " \n",
    "# Function getting_identical_header_records fetches the fasta sequences with identical headers\n",
    "def getting_identical_header_records(records, identical_headers):    \n",
    "    # Looping over each fasta record and checking for sequences with identical headers\n",
    "\n",
    "    for iteration, record in enumerate(records):\n",
    "        header = record.description\n",
    "        if header in identical_headers:\n",
    "            identical_headers[header].append(record)\n",
    "        \n",
    "    return identical_headers        \n",
    "    \n",
    "# Function getting_identical_header fetches only the identical headers\n",
    "def getting_identical_header(records):\n",
    "    # Looping over each fasta record and storing the headers along with their counts in a dictionary\n",
    "    header_counts = {} # This dictionary stores the headers along with their counts\n",
    "\n",
    "    for record in records:\n",
    "        header = record.description\n",
    "        if header not in header_counts.keys():\n",
    "            header_counts[header] = 1\n",
    "        else:\n",
    "            header_counts[header] += 1\n",
    "    \n",
    "    # fetching only the identical headers from the dictionary header_counts\n",
    "    identical_headers = {} # This list stores the identical headers\n",
    "\n",
    "    for header in header_counts:\n",
    "        if header_counts[header] > 1:\n",
    "            identical_headers[header] = []\n",
    "    \n",
    "    return identical_headers\n",
    "\n",
    "# Calling main function\n",
    "main(input_fasta)\n",
    "        \n",
    "        \n",
    "        "
   ]
  }
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