from Bio.SeqUtils import gc_fraction

from Bio.SeqUtils import MeltingTemp

from Bio.Seq import Seq

# Given DNA sequence
sequence = Seq("AAGCTATGGTGCTCTGTCCCATCACGCGGACCCGTGCACGCTGACGTTACTCCATAATCATGACGCTTACATTTCCGCAAGGCGCCCAATAGCCTTAGCTTGCCTCTGGACCCTACCTAAACTACTGCTGGGGAAATCCGAAAGGGCTGTAGGGGTGGGAGAACGCGTAGACGGTTCTCGTCTAGGTGCGGGTTATGAGTTCCGGGACGCCGGTGAAACCGGTAAGGGCTCCATGATATATAGGGAGGTGCAACTCTCTAAGACTCCACACCCACACTGGTAAAGAATTACCACTGCCCAATGGGCGGGCGGGAATTAGAACGAAGCATGCGTCCTTAATACGGGGAATGAATGATATGATGAACATAGGGCGTGTTACGTATACACACCCTATACCGAGTATTTGTTGCGCCTTCTCTTCAATGCACTGTCGTTGAACAGTTCCTATACTACGTGTGTGCCGAACCCACGATCCTCGTACCCCCTCCCCGGGACATCAG")
#sequence = Seq("AAGCTATGGT GCTCTGTCCC ATCACGCGGA CCCGTGCACG CTGACGTTAC TCCATAATCA TGACGCTTAC ATTTCCGCAA GGCGCCCAAT AGCCTTAGCT TGCCTCTGGA CCCTACCTAA ACTACTGCTG GGGAAATCCG AAAGGGCTGT AGGGGTGGGA GAACGCGTAG ACGGTTCTCG TCTAGGTGCG GGTTATGAGT TCCGGGACGC CGGTGAAACC GGTAAGGGCT CCATGATATA TAGGGAGGTG CAACTCTCTA AGACTCCACA CCCACACTGG TAAAGAATTA CCACTGCCCA ATGGGCGGGC GGGAATTAGA ACGAAGCATG CGTCCTTAAT ACGGGGAATG AATGATATGA TGAACATAGG GCGTGTTACG TATACACACC CTATACCGAG TATTTGTTGC GCCTTCTCTT CAATGCACTG TCGTTGAACA GTTCCTATAC TACGTGTGTG CCGAACCCAC GATCCTCGTA CCCCCTCCCC GGGACATCAG")
# 1. Calculate the frequency of each nucleotide base (A, T, C, G)
nucleotide_freq = {'A': sequence.count('A'), 'T': sequence.count('T'), 'C': sequence.count('C'), 'G': sequence.count('G')}
print("Frequency of each nucleotide base:", nucleotide_freq)

# 2. Give the number of nucleotides in the sequence
num_nucleotides = len(sequence)
print("Number of nucleotides:", num_nucleotides)

# 3. What is the length of the sequence?
sequence_length = len(sequence.replace(" ", ""))
print("Length of the sequence:", sequence_length)

# 4. Calculate the GC content of the DNA sequence file
gc_content = 100 * (sequence.count('G') + sequence.count('C')) / len(sequence)
gc_content1 = gc_fraction(sequence) * 100
print("GC content of the sequence:", gc_content)
print("GC content of the sequence:", gc_content1)

# 5. Give the reverse complement of the first line of the sequence
first_line = Seq("AAGCTATGGT")
reverse_complement = first_line.reverse_complement()
complement = first_line.complement()
print("Sequence of the first line:", first_line)
print("Complement of the first line:", complement)
print("Reverse complement of the first line:", reverse_complement)

# 6. Count each codon (3-nucleotide sequences) in the file
codon_count = {}
for i in range(0, len(sequence), 3):
    codon = sequence[i:i+3].replace(" ", "")
    codon_count[codon] = codon_count.get(codon, 0) + 1
print("Codon count:", codon_count)

# 7. What is the melting temperature (Tm) of the sequence?
#melting_temperature = Seq(sequence.replace(" ", "")).melting_temperature()
melting_temperature1 = MeltingTemp.Tm_Wallace(sequence)
melting_temperature2 = MeltingTemp.Tm_GC(sequence)
melting_temperature3 = MeltingTemp.Tm_NN(sequence)
print("Melting temperature of the sequence by using the Rule of thumb:", melting_temperature1)
print("Melting temperature of the sequence by using the GC melting temperature:", melting_temperature2)
print("Melting temperature of the sequence by using the Nearest-neighbor melting temperature:", melting_temperature3)

# 8. Create a text file containing a list of 5 DNA sequences in Python.
# Write a Python script to read the file and print the length of each sequence
with open("dna_sequences.txt", "w") as file:
    sequences = ["AAGCTATGGT", "GCTCTGTCCC", "ATCACGCGGA", "CCCACACTGG", "TAAAGAATTA"]
    for seq in sequences:
        file.write(seq + "\n")

# Read the file and print the length of each sequence
with open("dna_sequences.txt", "r") as file:
    for line in file:
        print("Length of sequence:", len(line.strip()))