Python programs

# Build a Translator

def translate(phrase):
    translation = ""
    for letter in phrase:
        if letter in "AEIOUaeiou":
            if letter.isupper():
                translation = translation + "K"
            else:
                translation = translation + "k"
        else:
            translation = translation + letter
    return translation

print(translate(input("enter a phrase")))

# Guessing game

secret_word = "giraffe"
guess = ""
guess_count = 0
guess_limit = 3
out_of_guesses = False

while guess != secret_word and not (out_of_guesses):
    if guess_count < guess_limit:
        guess = input ("Enter guess:")
        guess_count += 1
    else:
        out_of_guesses = True

if out_of_guesses:
    print("You lose")
else:
    print("You win")

# Caculator

num1 = float(input("Enter first number:"))
op = input("Enter operator:")
num2 = float(input("Enter second number:"))

if op == "+":
    print(num1 + num2)
elif op == "-":
    print (num1 - num2)
elif op == "/":
    print (num1 / num2)
elif op == "*":
    print (num1 * num2)
else:
    print ("Invalid operator")

# Lengte van de uitgeschreven input (voorbeeld primer sequentie)

Seq_primer = input("Enter primer sequence:")
print("length nucleotide primer sequence is:", len(Seq_primer), "nucleotides long")

# code die nummers in succesie verteld en een eindantwoord heeft

Leeftijd = 0
while Leeftijd <= 26:
    print(Leeftijd)
    Leeftijd += 1
if Leeftijd == 27:
    print("Jeetje wat oud")

# DNA to RNA

def DNA_to_RNA(DNA):
    DNA = DNA.upper()
    RNA = DNA.replace("T","U")
    return RNA

print(DNA_to_RNA(input("DNA sequence:")))

# RNA to DNA

def RNA_to_DNA(RNA):
    RNA = RNA.upper()
    DNA = RNA.replace("U","T")
    return DNA

print(RNA_to_DNA(input("RNA sequence:")))

# Reverse complement DNA

DNA = input("Please enter your DNA sequence")

DNA_upper = DNA.upper()
DNA_upper_reversed = DNA_upper[::-1]
for i in DNA_upper_reversed:
    if(i == "A"):print ("T", end ="")
    elif (i == "T"):print ("A", end ="")
    elif (i == "C"):print("G", end ="")
    elif (i == "G"):print("C", end ="")

# Nucleotide counter

DNA = input("Enter DNA sequence:")

Upper_DNA = DNA.upper()
A = Upper_DNA.count("A")
T = Upper_DNA.count("T")
C = Upper_DNA.count("C")
G = Upper_DNA.count("G")
print("The number of A in your DNA sequence is:", A)
print("The number of T in your DNA sequence is:", T)
print("The number of C in your DNA sequence is:", C)
print("The number of G in your DNA sequence is:", G)
print("The GC ratio of your DNA sequence is:",(G+C)/(G+C+T+A)*100, "procent!")

# Digestion enzym code

DNA0 = input("Enter DNA sequence:")
seq = DNA0.upper()
enz0 = input("Enter the enzyme name:")
enz = enz0.upper()

y= seq[0]
y_minus = 0

restriction_site = ""
restriction_site = 0
fragment = ""
enz = ""

def digestion (seq,enz):
    if (enz == "XBAI"): recognition_site = "TCTAGA"
    elif (enz == "ECORI"): recognition_site = "GAATTC"
    else:
        print("Enzym niet herkend")
    fragment = (seq.split(recognition_site))
    print("Upon digesting your DNA with "+ enz +", the following DNA fragments")
    for No_fr, i in enumerate(fragment):
        print(No_fr,i, end= "\n")
    str_regDNA0 = "(_^_)".join(map(str,fragment))
    str_regDNA1 = str(str_regDNA0[0:-1])
    print("\nThe map of your DNA sequence after this digestion would look like this")
    return(str_regDNA1)

digestion(DNA0, enz0)

# Module DNA naar AMINOZUUR
userDNA= str(input("Enter your DNA sequence:"))
Codon_triplet_data = ([userDNA[start : start+3]for start in range(0,len(userDNA),3)])

AA_dictionary = {
        'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M',
        'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T',
        'AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K',
        'AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R',
        'CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L',
        'CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P',
        'CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q',
        'CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R',
        'GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V',
        'GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A',
        'GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E',
        'GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G',
        'TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S',
        'TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L',
        'TAC': 'Y', 'TAT': 'Y', 'TAA': '*', 'TAG': '*',
        'TGC': 'C', 'TGT': 'C', 'TGA': '*', 'TGG': 'W', }

for codon in Codon_triplet_data:
    for item in AA_dictionary:
        if codon == item:
             print (AA_dictionary[item],end = "")


# Working with strings
phrase = "Giraffe Academy"
print(phrase.lower())
print(phrase + " is cool")
print (phrase.isupper())
print(phrase.upper().isupper())
print(len(phrase))
print(phrase[0])
print(phrase.index("Acad"))
print(phrase.replace("Giraffe", "Elephant"))

#Working with numbers
print(3 + 4.5)
print(3*(4+5))
print(10 % 3)

from math import *
my_num = -4
print(my_num)
print(max(4,6))
print(min(4,6))
print(round(5.768))
print(floor(4.7))
print(ceil(3.2))
print(sqrt(36))

#If statements

Is_male = True
Is_tall = False

if Is_male and Is_tall:
    print("you are a tall male")
elif Is_male and not Is_tall:
    print("you are a short male")
elif not Is_male and Is_tall:
    print("you are not a male but are tall")
else:
    print("you are either not male and not tall")

# Dictionary

Monthconversions = {
    "Jan":"January",
    "Feb":"February",
    "Mar": "March",
}

print(Monthconversions["Feb"])

#For loop

friends = ["jim","KAREN","kevin"]

for friend in friends:
    if friend.isupper():
        print ("Big Friend")
    else:
        print ("Small friend")

for index in range(5): # range means numbers
    if index == 0:
        print ("first")
    elif index == 1:
        print ("second")
    elif index == 2:
        print ("third")
    elif index == 3:
        print ("fourth")
    else:
        print ("last")

#Exponent Function

def raise_to_power(base_num, pow_num):
    result = 1
    for index in range(pow_num):
        result = result * base_num
    return result

print(raise_to_power(3,6))

# Biopython modules Chapter 3

# GC Counting with Biopython
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
my_seq = Seq(input("ENTER DNA SEQUENCE:"), IUPAC.unambiguous_dna)
print(GC(my_seq))

# counting elements in Sequence

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
my_seq = Seq(input("ENTER DNA SEQUENCE"), IUPAC.unambiguous_dna)
for index, letter in enumerate(my_seq):
    print("%i %s" % (index, letter))
print(len(my_seq)) # print de totale lengte van de sequentie
print(my_seq[0]) # print een exacte aangegeven element uit

# Sequence slicing

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC", IUPAC.unambiguous_dna)
print(my_seq[2:12])

# Adding sequences

from Bio.Seq import Seq
from Bio.Alphabet import generic_nucleotide
from Bio.Alphabet import IUPAC
nuc_seq = Seq(input("Enter first sequence"), generic_nucleotide)
dna_seq = Seq(input("Enter second sequence"), IUPAC.unambiguous_dna)
print(nuc_seq + dna_seq)

from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", generic_dna), Seq("GGTT", generic_dna)]
sum(list_of_seqs, Seq("", generic_dna))

# changing case

from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
dna_seq = Seq("acgtACGT", generic_dna)
print(dna_seq.upper())
print(dna_seq.lower())

# Sequences in (reverse) complements

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
my_seq = Seq("GAAAAAC", IUPAC.unambiguous_dna)
print(my_seq.complement())
print(my_seq.reverse_complement())

# TRANSCRIPTION

# DNA TO mRNA

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
coding_dna = Seq("", IUPAC.unambiguous_dna)
template_dna = coding_dna.reverse_complement()
print(template_dna.reverse_complement().transcribe())

# mRNA to DNA

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", IUPAC.unambiguous_rna)
print(messenger_rna.back_transcribe())

# TRANSLATION

# mRNA to Protein

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", IUPAC.unambiguous_rna)
print(messenger_rna.translate())

# DNA to protein

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", IUPAC.unambiguous_dna)
print(coding_dna.translate())

# Gene translation

from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
gene = Seq("GTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCA" + \
           "GCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGAT" + \
           "AATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACAT" + \
           "TATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACCGCCGCGCCACCAT" + \
           "AAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA", generic_dna)
print(gene.translate(table="Bacterial"))

# Translation tables

from Bio.Data import CodonTable
standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
mito_table = CodonTable.unambiguous_dna_by_name["Vertebrate Mitochondrial"]
print(standard_table)
print(standard_table.start_codons)

# Comparing objects

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
seq1 = Seq(input("Enter DNA sequence 1"), IUPAC.unambiguous_dna)
seq2 = Seq(input("Enter DNA sequence 2"), IUPAC.ambiguous_dna)
print(str(seq1) == str(seq2))