organisms = ['Pan troglodytes', 'Gallus gallus', 'Xenopus laevis', 'Vipera palaestinae']

print(organisms[0])
print(organisms[2])

organisms_classes = {'Pan troglodytes': 'Mammalia', 'Gallus gallus': 'Aves', 'Xenopus laevis': 'Amphibia', 'Vipera palaestinae': 'Reptilia'}

observations = {'Equus zebra': 143,
                'Hippopotamus amphibius': 27,
                'Giraffa camelopardalis': 71,
                'Panthera leo': 112}

print(organisms_classes['Pan troglodytes'])
print(organisms_classes['Gallus gallus'])

organisms_classes['Pan troglodytes'] = 'Mammals'
print(organisms_classes['Pan troglodytes'])

organisms_classes['Danio rerio'] = 'Actinopterygii'
print(organisms_classes['Danio rerio'])

for organism in organisms:
    print(organism)

for organism in organisms_classes:
    print(organism, 'belongs to the', organisms_classes[organism], 'class.')

for animal in observations:
    if observations[animal] > 50:
        observations[animal] = True
    else:
        observations[animal] = False
print(observations)

'Vipera palaestinae' in organisms_classes

'Bos taurus' in organisms_classes

new_organism = ['Vipera palaestinae', 'Bos taurus']
for organism in new_organism:
    if organism in organisms_classes:
        print(organism, 'belongs to the', organisms_classes[organism], 'class.')
    else:
        print(organism, 'not found in dictionary.')

# Create dictionary
details_dict = {'Name': 'James Watson', 'Address': 'Cambridge', 'Phone': '12345678'}

# print sentence
print("My name is",details_dict['Name'],"I live in",details_dict['Address'],"My phone number is",details_dict['Phone'])

# Create codons dictionary
bases = ['t', 'c', 'a', 'g']
codons = [a+b+c for a in bases for b in bases for c in bases]
amino_acids = 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'
codon_table = dict(zip(codons, amino_acids))

# Sequence list
seq_list = ["atg","caa","ggc","ata","tca","tgg","cga","agg","cct","taa"]

# iterate on list and translate
for codon in seq_list:
    print(codon_table[codon], end='')

x = 3
y = 2*x + 6
print(y)

def function_name(input1, input2, input3,...):
    # some processes
    .
    .
    .
    return output

def linear1 (x):
    y = 2*x + 6
    return y

result1 = linear1(3)
print(result1)

result2 = linear1(7)
print(result2)

def concat_to_sequences(sequence_list, sequence_to_concat):
    new_list = []
    for seq in sequence_list:
        new_list.append(seq + sequence_to_concat)
    return new_list

my_sequences = ['AGTTAGAGTTA', 'TTACCAGTG', 'GGCAACTTTAGG']
new_sequences = concat_to_sequences(my_sequences, 'GGG')
print(my_sequences)
print(new_sequences)

def complement(sequence):
    transcript_dict = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G'}
    complement = ''
    for base in sequence:
        complement += transcript_dict[base]
    return complement

my_dna = 'ACGCTATTAGAGGGCGAGAAGCTAGAGGA'
my_complement = complement(my_dna)
print(my_complement)

def reverse_sequence(sequence):
    reversed_seq = ''
    seq_as_list = list(sequence)
    for base in reversed(seq_as_list):
        reversed_seq += base
    return reversed_seq

my_reverse_complement = reverse_sequence(my_complement)
print(my_reverse_complement)

def reverse_complement(sequence):
    complement_seq = complement(sequence)
    reverse_complement = reverse_sequence(complement_seq)
    return reverse_complement

print(reverse_complement(my_dna))

def print_reverse_complement(sequence):
    complement_seq = complement(sequence)
    reverse_complement = reverse_sequence(complement_seq)
    print(reverse_complement)

print_reverse_complement(my_dna)

my_reverse_complement = reverse_complement(my_dna)
final_sequence = "ATG" + my_reverse_complement + "TAA"
print(final_sequence)

def reverse_complement(sequence):
    """
    Receives a string of DNA sequence and returns a string of it's reverse complement
    """
    complement_seq = complement(sequence)
    reverse_complement = reverse_sequence(complement_seq)
    return reverse_complement

help(reverse_complement)

# define function
def first_5_longer_sequence(seq1,seq2):
    if len(seq1) > len(seq2):
        return seq1[:5]
    else:
        return seq2[:5]
    
# Test function
sequence1 = "aggtctcggatataggcgcgatattta"
sequence2 = "ttaagccacgcttcggatta"
first_5 = first_5_longer_sequence(sequence1, sequence2)
print(first_5)

# define function
def odd_bases(seq):
    odd_bases_list = []
    for i in range(len(seq)):
        if i % 2 == 0:
            odd_bases_list.append(seq[i])    
    return odd_bases_list

# or another option
def odd_bases(seq):
    odd_bases_list = list(seq[::2])   
    return odd_bases_list

# Test function
odd_bases_list = odd_bases("aggtctcggatataggcgcgatattta")
print(odd_bases_list)

def len(lst):
    .
    .
    .

def pythagoras(a,b):
    hypo_square = a**2 + b**2
    hypo = hypo_square**0.5

pythagoras(3,5)
print(hypo)

def pythagoras(a,b):
    hypo_square = a**2 + b**2
    hypo = hypo_square**0.5
    print(hypo)
pythagoras(3,5)

def pythagoras(a,b):
    hypo_square = a**2 + b**2
    hypo = hypo_square**0.5
    return(hypo)

result = pythagoras(3,5)
print(result)