'''
Jon Beck
translate.py

A program to read a mRNA sequence from a fasta file, pre-process it
by removing the start codon, translate it according to the standard 
genetic code, and print the resulting amino acid sequence to the screen.

This program assumes the sequence in the fasta file appears 5' to 3'.
'''
from rna2aa import rna2aa
from readfasta import readfasta

def main():
    # read in the rna from disk
    # we assume there is exactly one sequence in the fasta file
    rnainfo = readfasta('maizefragment.fasta')
    rnasequence = rnainfo[0][2]

    # remove the start codon
    rnasequence = rnasequence[3:]

    # we now assume that rnasequence contains a stop codon an exact multiple
    # of 3 nucleotides from the beginning

    # translate it
    aasequence = rna2aa(rnasequence)

    # print the results
    print('The resulting amino acid sequence is:')
    print(aasequence)

main()