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#!/usr/bin/env python3

import sys

filename = sys.argv[1]

totfile = open(filename).read()

contains_aminoacid = False
header = ''
type_file = ''

for header in totfile:
    if header.startswith('>'):
        print(header,'/n')

for line in totfile:
    if not line.startswith('>'):
        pass
        stripped = line.strip()
        for characters in stripped:
            if characters not in ['A','T','C','G','U']
                contains_aminoacid = True
                if contains_aminoacid == True:
                    type_file = "aminoacid"
                    print(type_file)
                        break

start_num = input("On what character would you like to start the translation?\n")
start_num = int(start_num)

count = 1
templist = []

if contains_aminoacid == False:
    for char in stripped:
        count += 1
        templist.append(char)
        if count == start_num:
            tempstring = ''.join(templist)
            string_ready = stripped.replace(tempstring, '')
        elif count > start_num:
            break

tripletlist = []
templist = []

if contains_aminoacid == False:
    for char in string_ready:
        templist.append(char)
        if len(templist) == 3:
            triplet = "".join(templist)
            tripletlist.append(triplet)
            templist = []
        else:
            continue


aminoacid_codons = {"GCT":"A", "GCC":"A", "GCA":"A", "GCG":"A", "CGT":"R",
                    "CGC":"R", "CGA":"R", "CGG":"R", "AGA":"R", "AGG":"R",
                    "AAT":"N", "AAC":"N", "GAT":"D", "GAC":"D", "TGT":"C",
                    "TGC":"C", "CAA":"Q", "CAG":"Q", "GAA":"E", "GAG":"E",
                    "GGT":"G", "GGC":"G", "GGA":"G", "GGG":"G", "CAT":"H",
                    "CAC":"H", "ATT":"I", "ATC":"I", "ATA":"I", "TTA":"L",
                    "TTG":"L", "CTT":"L", "CTC":"L", "CTA":"L", "CTG":"L",
                    "AAA":"K", "AAG":"K", "ATG":"M", "TTT":"F", "TTC":"F",
                    "CCT":"P", "CCC":"P", "CCA":"P", "CCG":"P", "TCT":"S",
                    "TCC":"S", "TCA":"S", "TCG":"S", "ATG":"S", "AGC":"S",
                    "ACT":"T", "ACC":"T", "ACA":"T", "ACG":"T", "TGG":"W",
                    "TAT":"Y", "TAC":"Y", "GTT":"V", "GTC":"V", "GTA":"V",
                    "GTG":"V"}

protein_file = open("proteinseq.fasta", 'r+')

for item in tripletlist:
    if item in aminoacid_codons:
        protein_file.write(aminoacid_codons[item])