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"""
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
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