#!/usr/bin/env python
# coding: utf-8

# In[1]:


genetic_code = {
    # this was adapted from 
    # https://gitlab.com/RebelCoder/dna-toolset/-/blob/90e8d9249c6dcc82a850aa854da4baabef98ee6f/structures.py
    "GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A",
    "TGT": "C", "TGC": "C",
    "GAT": "D", "GAC": "D",
    "GAA": "E", "GAG": "E",
    "TTT": "F", "TTC": "F",
    "GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G",
    "CAT": "H", "CAC": "H",
    "ATA": "I", "ATT": "I", "ATC": "I",
    "AAA": "K", "AAG": "K",
    "TTA": "L", "TTG": "L", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L",
    "ATG": "M",
    "AAT": "N", "AAC": "N",
    "CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P",
    "CAA": "Q", "CAG": "Q",
    "CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "AGA": "R", "AGG": "R",
    "TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "AGT": "S", "AGC": "S",
    "ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T",
    "GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V",
    "TGG": "W",
    "TAT": "Y", "TAC": "Y",
    "TAA": "*", "TAG": "*", "TGA": "*"
}


# In[2]:


'TTTTATGATGT'.index('ATG')


# In[3]:


list(range(4, 25, 3))


# In[4]:


test_sequence = 'TTTTATGACCT'
print(test_sequence[10:10+3])


# In[5]:


genetic_code['AGA']


# In[11]:


'AAA' not in 'ACGAAAT'


# In[22]:


def translate(sequence, genetic_code):
    protein = []
    
    if 'ATG' not in sequence:
        return protein
    
    first_codon_position = sequence.index('ATG')
    
    sequence_length = len(sequence)
    
    for codon_start in range(first_codon_position, sequence_length, 3):
        codon = sequence[codon_start:codon_start+3]
        if len(codon) == 3:
            try:
                amino_acid = genetic_code[codon]
            except KeyError:
                raise KeyError(codon + " is not present in the genetic code.")
            if amino_acid == '*':
                return protein
            protein.append(amino_acid)
    
    return protein


# In[23]:


translate("AGGTACGTGGAACGTACGTGACCGATGGACCACACUCATTGAGTGTGTACACACACGTGTGTGTGACACAACAAC", genetic_code)


# In[ ]: