one_case.py

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

stop_letters = ["TAA", "TAG", "TGA"]

example = "ENST0000039045,ATGGTCCTGAAATTCTCCGTGTCCATTCTTTGGATTCAGTTGGCATGGGTGAGCACCCAGCTGCTGGAGCAGAGCCCTCAGTTTCTAAGCATCCAAGAGGGAGAAAATCTCACTGTGTACTGCAACTCCTCAAGTGTTTTTTCCAGCTTACAATGGTACAGACAGGAGCCTGGGGAAGGTCCTGTCCTCCTGGTGACAGTAGTTACGGGTGGAGAAGTGAAGAAGCTGAAGAGACTAACCTTTCAGTTTGGTGATGCAAGAAAGGACAGTTCTCTCCACATCACTGCAGCCCAGCCTGGTGATACAGGCCTCTACCTCTGTGCAGGAG"


def protein_translation(single_line):
	"This function translates DNA into proteins"
	name, seq = single_line.rstrip("\n").split(",")
	letters = []

	for i in range(0, len(seq), 3):
	    letter = seq[i:i+3]
	    letters.append(letter)
	    if letter in stop_letters:
	    	break

	    # print letter
	print letters


    # with open("protein_sequences.fasta", 'w') as outfile:
    #     for strain in protein_seq:
    #         outfile.write("{}\n".format(protein_seq[strain])) #writes value (sequence) to sequence line

protein_translation(example)