demo/create_csv.py

"""
Create CSV version of the demo database for easy import testing.
"""
import csv
import os

# Same sequences as in create_demo_db.py
UTR5_BETAGLOBIN = (
    "ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGAC"
    "TCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGT"
)[:80]

UTR5_EMCV = "GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGAGCCACCATG"
KOZAK_TEV = "GCCACC"

UTR3_BETAGLOBIN = (
    "GCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTA"
    "AACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATT"
    "TTCATTGCAATGATGTATTTAAATTATTTCTGAATATTTTACTAAAAATAAATGTTTTTTAT"
)[:100]

UTR3_ALBUMIN = (
    "AATAAAGATCTTTATTTTCATTAGATCTGTGTGTTGGTTTTTTGTGTGAATCGATAGTACTA"
    "AATACTTTTCAGACACCAGAAATGCAGAGCAGTTCAGAGGCAGAGCCATCTATTGCTTACAT"
)[:100]

POLYA_120 = "A" * 120
POLYA_60 = "A" * 60

CDS_EGFP = (
    "ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAG"
    "TAA"
)

CDS_MCHERRY = (
    "ATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAG"
    "TAA"
)

CDS_LUC2 = (
    "ATGGAAGATGCCAAAAACATTAAGAAGGGCCCAGCGCCATTCTACCCACTCGAAGACGGGAC"
    "CGCCGGCGAGCAGCTGCACAAAGCCATGAAGCGCTACGCCCTGGTGCCCGGCACCATCGCCT"
    "TTACCGACGCACATATCGAGGTGGACATTACCTACGCCGAGTACTTCGAGATGAGCGTTCGG"
    "CTGGCAGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATCGGATCGTGGTGTGCAGCGA"
    "GAATAGTCTGGAGAAGATCCTGCTGAACAAAGGCCTGCCTGTAGCCGGCCTTTTCCTCCTGG"
    "AAGAGCTGCGGCAGCAGTTCCAGAAGGCCCGGGAGCAGATGTTCACCTTCGTGCTCGATCTG"
    "GAGGAAATGACCGCCGAAGAGGCGATTGAGAATCTGGTATTCGAGCAGTATGGAATCGACCA"
    "TTATCTTGATAACCCACAATGCCTGCATGACCTGGTGCATCTGGAACCCCGAGGTCAATGTG"
    "GAAGAGTTCCTGGAAAAGCTGCTGAAGGACGGTATCATCATGTTCAGCATCCATGGTTATGG"
    "CTACATCCTGGGGCCCGGAACCAACTTCGATCTGGAGCGCATGATCAAGCGCGATGGGGAG"
    "GTGGATATGGCCCTGATTAAGGTGTCGATGGAGCAGGCCGGCATCGACCCCGATGAGGCCGG"
    "AGCCATTCGGCTGTACAAGCTGATGAAGGATAAG"
    "TAA"
)[:900]
while len(CDS_LUC2) % 3 != 0:
    CDS_LUC2 = CDS_LUC2[:-3] + "TAA"

CDS_SPIKE_RBD = (
    "ATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTGTCCTCCCAGGTGTGCAACCTGACCACCAG"
    "AACCCAGCTGCCCCCCGCCTACACCAACTCCTTCACCCGGGGCGTGTACTACCCCGACAAGG"
    "TGTTCCGCTCCTCCGTGCTGCACTCCACCCAGGACCTGTTTCTGCCCTTTTTCTCCAACGTG"
    "ACCTGGTTCCACGCCATCCACGTGTCCGGCACCAACGGCACAAAGCGGTTCGACAACCCCGTG"
    "CTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCCGGGGCTG"
    "GATCTTCGGCACCACCCTGGACTCCAAGACCCAGTCCCTGCTGATCGTGAACAACGCCACCA"
    "ACGTGGTCATCAAGGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGGGCGTCTACTAC"
    "CACAAGAACAACAAGTCCTGGATGGAGTCCGAGTTCCGGGTGTACTCCTCCGCCAACAACTG"
    "CACCTTTGAGTACGTGTCCCAGCCCTTTCTGATGGACCTGGAGGGCAAACAGGGCAACTTCA"
    "AGAACCTGCGCGAGTTTGTGTTTAAGAACATCGACGGCTACTTCAAGATCTACAGCAAGCAC"
)
CDS_SPIKE_RBD = CDS_SPIKE_RBD[:len(CDS_SPIKE_RBD) - len(CDS_SPIKE_RBD) % 3]
CDS_SPIKE_RBD = CDS_SPIKE_RBD[:-3] + "TAA"

CDS_EPO = (
    "ATGGGGGTGCACGAATGTCCCGCCTGGCTGTGGCTGCTGCTGTCGCTGCCGTTCTCTGTGCT"
    "GCCCGCCCGCGCCGTCCTCACCGTCAACTTCCCGCACCCTGCTTCCACGCCTCAGAGTCCTG"
    "GAGAGGTACCTCTTGGAGGCCAAGGAGGCCGAGAATATCACGACGGGCTGTGCTGAACACTGC"
    "AGCTTGAATGAGAATATCACGGTGCGCTTTCCACGCCTCATTTGCGACAGCTTTGTTCGTGG"
    "TCAGGCCGTGGTCAGCTCCGATGAGGTCTTCAGGGCCCCTGTCCTCCTGCAGCTGGAATCCT"
    "GGCAGCGTCTCAGCCCCTGCAGCCAGCCCTCCCAGCTGCCCTCAGCCACCTGTCCCGCCTGCT"
    "CCAGAGCCTGGAGAACTTCTACCAGCCTCTGGAGCAGCTCCAGGAAGTGATCCAGGAGATGAG"
    "CAAGCTGTCCGCCACGGCCGTGGAGGTCTTGGCCAGTAAGCCGGAG"
    "TAA"
)
CDS_EPO = CDS_EPO[:len(CDS_EPO) - len(CDS_EPO) % 3]
if not CDS_EPO.endswith("TAA") and not CDS_EPO.endswith("TAG") and not CDS_EPO.endswith("TGA"):
    CDS_EPO = CDS_EPO[:-3] + "TAA"

CDS_FIX = (
    "ATGCAGCGCGTGAACATGATCATGGCCTCCCTGTGGCTGTGCTTCGTGGCCCTGTGGCAGGC"
    "TGGCAACCCCAGAGAAGTACCTGTTCAAGAACGGCGACCAGCGGCCCAACAAGGAGATCCCCA"
    "AGAGCATCATCCTGGAGGAGTTCAAGGCCTTCTTCTCCACCTTCATCAACCGGAAGATGATCA"
    "AGCAGACCGACAAAGACCAGGTGATCAGCCTGGGCGGCAAGGACCAGGTGCTGATCCAGATGC"
    "AGCCCCAGGTGAGCAAGGACTTTGGCTTCAGCCTGTGCACCTGCCCCTGGGGCCACCCCAGCC"
    "CCTGCAGCAGCACATCCTGTACTTCCTGAACCAGAAGGCCAAACAGTTCCTGCTGCAGGACGAG"
    "AAGGTGAAGGGCATCAACCACTGCAAGGTGCGGGTGGCCCTGGAGCAGGACGGCAGCAAGGTG"
)
CDS_FIX = CDS_FIX[:len(CDS_FIX) - len(CDS_FIX) % 3]
CDS_FIX = CDS_FIX[:-3] + "TAA"

FULL_MRNA_EGFP = UTR5_BETAGLOBIN + KOZAK_TEV + "ATG" + CDS_EGFP[3:] + UTR3_BETAGLOBIN + POLYA_120
FULL_MRNA_MCHERRY = UTR5_EMCV + CDS_MCHERRY + UTR3_ALBUMIN + POLYA_60

# Build CSV rows
CSV_DATA = [
    {
        'id': 1,
        'gene_name': 'eGFP-hBG-UTRs',
        'five_prime_utr': UTR5_BETAGLOBIN,
        'cds': CDS_EGFP,
        'three_prime_utr': UTR3_BETAGLOBIN,
        'poly_a_tail': POLYA_120,
        'full_mrna': '',
        'target_protein': 'Enhanced GFP',
        'organism': 'Aequorea victoria',
        'expression_system': 'HEK293T',
        'gc_target_percent': 52.4,
        'notes': 'Human beta-globin UTRs. Classic reporter construct for mRNA transfection.'
    },
    {
        'id': 2,
        'gene_name': 'mCherry-AlbUTR',
        'five_prime_utr': UTR5_BETAGLOBIN,
        'cds': CDS_MCHERRY,
        'three_prime_utr': UTR3_ALBUMIN,
        'poly_a_tail': POLYA_120,
        'full_mrna': '',
        'target_protein': 'mCherry red fluorescent protein',
        'organism': 'Discosoma sp.',
        'expression_system': 'CHO',
        'gc_target_percent': 50.1,
        'notes': 'Albumin 3\'UTR for extended expression. Good cell viability.'
    },
    {
        'id': 3,
        'gene_name': 'Luc2-reporter',
        'five_prime_utr': UTR5_EMCV,
        'cds': CDS_LUC2,
        'three_prime_utr': UTR3_ALBUMIN,
        'poly_a_tail': POLYA_60,
        'full_mrna': '',
        'target_protein': 'Firefly luciferase',
        'organism': 'Photinus pyralis',
        'expression_system': 'Huh-7',
        'gc_target_percent': 53.8,
        'notes': 'Bioluminescence reporter. Used for LNP screening.'
    },
    {
        'id': 4,
        'gene_name': 'SpRBD-v1',
        'five_prime_utr': UTR5_BETAGLOBIN,
        'cds': CDS_SPIKE_RBD,
        'three_prime_utr': UTR3_ALBUMIN,
        'poly_a_tail': POLYA_120,
        'full_mrna': '',
        'target_protein': 'SARS-CoV-2 Spike RBD',
        'organism': 'SARS-CoV-2',
        'expression_system': 'HEK293T',
        'gc_target_percent': 55.2,
        'notes': 'Vaccine antigen candidate. Proline-stabilized RBD.'
    },
]

def create_csv():
    output_path = os.path.join(os.path.dirname(__file__), 'mrna_sequences.csv')

    with open(output_path, 'w', newline='') as f:
        fieldnames = ['id', 'gene_name', 'five_prime_utr', 'cds', 'three_prime_utr',
                      'poly_a_tail', 'full_mrna', 'target_protein', 'organism',
                      'expression_system', 'gc_target_percent', 'notes']
        writer = csv.DictWriter(f, fieldnames=fieldnames)
        writer.writeheader()
        writer.writerows(CSV_DATA)

    print(f'✓ Created {output_path}')
    print(f'  {len(CSV_DATA)} sequences exported')
    return output_path

if __name__ == '__main__':
    create_csv()