bioinformatics-in-python/main.py at main · busari-mcode/bioinformatics-in-python · GitHub

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# DNA Toolset/Code testing file
from dna_toolkit import *
from utilities import colored
import random

# Creating a random DNA Sequence for testing:
randDNAStr = ''.join([random.choice(Nucleotides)
                      for nuc in range(50)])

DNAStr = validateSeq(randDNAStr)

print(f'\nSequence: {colored(DNAStr)}\n')
print(f'[1] + Sequence Length: {len(DNAStr)}\n')
print(colored(f'[2] + Nucleotide Frequency: {countNucFrequency(DNAStr)}\n'))
print(f'[3] + DNA/RNA Transcription: {colored(transcription(DNAStr))}\n')

print(f"[4] + DNA String + Reverse Complement:\n5' {colored(DNAStr)} 3'")
print(f"   {''.join(['|' for c in range(len(DNAStr))])}")
print(f"3' {colored(reverse_complement(DNAStr)[::-1])} 5' [Complement]")
print(f"5' {colored(reverse_complement(DNAStr))} 3' [Rev. Complement]\n")

print(f"[5] + GC Content: {gc_content(DNAStr)}%\n")
print(f"[6] + GC Content in Subsection k=5: {gc_content_subsec(DNAStr, k=5)}\n")

print(
    f'[7] + Aminoacids Sequence from DNA: {translate_seq(DNAStr, 0)}\n')

print(
    f'[8] + Codon frequency (L): {codon_usage(DNAStr, "L")}\n')


# *************************************** LEARNING PHASE 3 *******************************************
# # DNA Toolset/Code testing file
# from DNAToolkit import *
# import random

# # Creating a random DNA Sequence for testing:
# randDNAStr = ''.join([random.choice(Nucleotides)
#                       for nuc in range(50)])

# DNAStr = validateSeq(randDNAStr)
# print(countNucFrequency(DNAStr))
# print(transcription(DNAStr))


# *************************************** LEARNING PHASE 2 *******************************************
# ****************Counting Nucleotides in the Validated random DNA String generated*************

# # DNA Toolset/Code testing file
# from DNAToolkit import *
# import random

# # Creating a random DNA Sequence for testing:
# randDNAStr = ''.join([random.choice(Nucleotides)
#                       for nuc in range(50)])

# DNAStr = validateSeq(randDNAStr)
# print(countNucFrequency(DNAStr))


# ************************ LEARNING PHASE 1 ******************************
# ****************Validate DNA Sequence*************

# # DNA Toolset/Code testing file
# from DNAToolkit import *

# # random DNA string
# rndDNAStr = "ATTTCGT"
# rndDNAStr2 = "ATTTCGTX"
# rndDNAStr3 = "AtCCgGGtGGt"

# print(validateSeq(rndDNAStr))
# print(validateSeq(rndDNAStr2))
# print(validateSeq(rndDNAStr3))