06.Translate_seqs.ipynb

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   "source": [
    "# In silico translation of DNA sequences to amino acid sequences "
   ]
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      "Defaulting to user installation because normal site-packages is not writeable\n",
      "Collecting biopython\n",
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      "\u001b[?25hRequirement already satisfied: numpy in /usr/lib/python3/dist-packages (from biopython) (1.21.5)\n",
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   "source": [
    "# Load packages \n",
    "from Bio import SeqIO\n",
    "from Bio.Seq import Seq\n",
    "import os\n",
    "\n",
    "# Input and output file names\n",
    "input_file = \"data/MCF7_ORFs_min18.fasta\"\n",
    "output_file = \"data/MCF7_altORFs_proteins.fasta\""
   ]
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     "text": [
      "Error: The file data/MCF7_altORFs_proteins.fasta doesn't exist. Creating the file...\n",
      "Translation completed. Protein sequences saved in data/MCF7_altORFs_proteins.fasta\n"
     ]
    }
   ],
   "source": [
    "# Check if output file exists; if not, raise an error\n",
    "if not os.path.exists(output_file):\n",
    "    print(f\"Error: The file {output_file} doesn't exist. Creating the file...\")\n",
    "    # Create an empty file\n",
    "    with open(output_file, 'w') as f:\n",
    "        pass\n",
    "\n",
    "# Open the output file for writing translated sequences\n",
    "with open(output_file, \"w\") as output_handle:\n",
    "    for record in SeqIO.parse(input_file, \"fasta\"):\n",
    "        nucleotide_seq = record.seq\n",
    "        protein_seq = nucleotide_seq.translate(to_stop=True)\n",
    "        output_handle.write(f\">{record.id}\\n{protein_seq}\\n\")\n",
    "\n",
    "print(f\"Translation completed. Protein sequences saved in {output_file}\")"
   ]
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   "execution_count": 3,
   "id": "d319ae42-32b1-41d6-8b3c-0497e05266b6",
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     "text": [
      "Nucleic acid Sequences\n",
      "Record ID: SRR6730014.4_ORF.1\n",
      "DNA Sequence: CTGCGCGTGCACGGCGCCACCCTCCCCCCGCCCCAGCCCGGCGCCGTGCGACTTTGCTCCTGCAACACACGCCCCCCCAACCCCCGCCCG\n",
      "\n",
      "Record ID: SRR6730014.5_ORF.1\n",
      "DNA Sequence: CTGCGCGTGCACGGCGCCTCCCTCCCCCCGCCCCAGCCCGGCGCCGTGCGACTTTGCTCCTGCACCACTCGCCCCCCCACCCCCCGCCCG\n",
      "\n",
      "Record ID: SRR6730014.6_ORF.1\n",
      "DNA Sequence: TTGCGCAGTCATTTTCAACACCGGCAATGCAGCAAAATCATCAGTGGAAATGTAAAAAAATACACATGGCCAGGCCCCAGCCCAAATCAC\n",
      "\n",
      "Record ID: SRR6730014.6_ORF.2\n",
      "DNA Sequence: CTGGGGCCTGGCCATGTGTATTTTTTTACATTTCCACTGATGATTTTGCTGCATTGCCGGTGT\n",
      "\n",
      "Record ID: SRR6730014.6_ORF.3\n",
      "DNA Sequence: TTGGGCTGGGGCCTGGCCATGTGTATTTTTTTACATTTCCAC\n",
      "\n",
      "Amino acid Sequences\n",
      "Record ID: SRR6730014.4_ORF.1\n",
      "Protein Sequence: LRVHGATLPPPQPGAVRLCSCNTRPPNPRP\n",
      "\n",
      "Record ID: SRR6730014.5_ORF.1\n",
      "Protein Sequence: LRVHGASLPPPQPGAVRLCSCTTRPPTPRP\n",
      "\n",
      "Record ID: SRR6730014.6_ORF.1\n",
      "Protein Sequence: LRSHFQHRQCSKIISGNVKKYTWPGPSPNH\n",
      "\n",
      "Record ID: SRR6730014.6_ORF.2\n",
      "Protein Sequence: LGPGHVYFFTFPLMILLHCRC\n",
      "\n",
      "Record ID: SRR6730014.6_ORF.3\n",
      "Protein Sequence: LGWGLAMCIFLHFH\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Check the first few sequences from the input and output file for visual inspection\n",
    "## Set of sequences (rows) to display\n",
    "num_sequences_to_display = 5  # Adjust this as needed\n",
    "\n",
    "## Read and print \n",
    "with open(input_file, \"r\") as input_handle:\n",
    "    records = SeqIO.parse(input_handle, \"fasta\")\n",
    "    print(f\"Nucleic acid Sequences\")\n",
    "    for i, record in enumerate(records):\n",
    "        if i >= num_sequences_to_display:\n",
    "            break\n",
    "        print(f\"Record ID: {record.id}\")\n",
    "        print(f\"DNA Sequence: {record.seq}\\n\")\n",
    "        \n",
    "with open(output_file, \"r\") as output_handle:\n",
    "    records = SeqIO.parse(output_handle, \"fasta\")\n",
    "    print(f\"Amino acid Sequences\")\n",
    "    for i, record in enumerate(records):\n",
    "        if i >= num_sequences_to_display:\n",
    "            break\n",
    "        print(f\"Record ID: {record.id}\")\n",
    "        print(f\"Protein Sequence: {record.seq}\\n\")"
   ]
  }
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