"""
This module contains methods for the RUST tool 
These are general purpose functions that are used in the RUST tool

"""
import sys


def stop_err(msg):
    sys.stderr.write("%s\n" % msg)
    sys.exit()


def mean_value(input_list):
    if len(input_list) == 0:
        return 0
    else:
        return sum(map(float, input_list)) / len(input_list)


def translate_dna(sequence):
    codontable = {
        "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",
    }
    proteinsequence = ""
    for n in range(0, len(sequence), 3):
        try:
            proteinsequence += codontable[sequence[n : n + 3]]
        except:
            proteinsequence += "X"
    return proteinsequence