import sys
import re

# patterns
pat = re.compile('chr.{1,2}:g\.([0-9]{1,100})[ATCGdi_].')
pat_sub = re.compile('(chr.{1,2}):g\.([0-9]{1,100})([ATCG]>[ATCG])')
pat_del = re.compile('(chr.{1,2}):g\.([0-9]{1,100})del([ATCG]{1,100})')
pat_ins = re.compile('(chr.{1,2}):g\.([0-9]{1,100})_([0-9]{1,100})ins([ATCG]{1,100})')

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

# function : translate a nucleotide sequence into amino acid sequence
def translate(seq, frame) :
    pro_seq = ''
    for i in range(frame, len(seq)-3, 3) :
        pro_seq += codon_table[seq[i:i+3]]
        if codon_table[seq[i:i+3]] == '-' :
            break
    return pro_seq

for frm_length in range(8,15) :
    in_mut = open(sys.argv[1], 'r')
    out_fi_name = sys.argv[2] + '_' + str(frm_length) + '.fasta'
    out_fi = open(out_fi_name, 'w')
    out_fi_list = []
    for line in in_mut :
        line = line.strip()
        if line[0] == '>' :
            ab_line = line
            ab_list = line[1:].strip().split('|')
            match_sub = pat_sub.search(ab_list[0])
            match_del = pat_del.search(ab_list[0])
            match_ins = pat_ins.search(ab_list[0])
            print ab_line
        else :
            aa_line = translate(line, int(ab_list[-1][0]))
            print aa_line
            if aa_line[-1] == '-' :
                aa_line = aa_line[:-1]
            if match_del :
                if ab_list[-1][2] == '-' :
                    nlc_mut_site = int(ab_list[3]) - int(match_del.group(2))
                    aa_mut_site = (nlc_mut_site - int(ab_list[-1][0])) / 3
                    if len(aa_line) - aa_mut_site >= frm_length :
                        aa_line = aa_line[:aa_mut_site+frm_length]
                    if aa_mut_site + 1 >= frm_length :
                        aa_line = aa_line[aa_mut_site - frm_length + 1:]
                    print aa_line
                    print len(aa_line)
                    for frames in range(len(aa_line) - frm_length + 1) :
                        new_frame = aa_line[frames:frames+frm_length]
                        out_fi_list.append(ab_line)
                        out_fi_list.append(new_frame)
                else :
                    nlc_mut_site = int(match_del.group(2)) - int(ab_list[2])
                    aa_mut_site = (nlc_mut_site - int(ab_list[-1][0])) / 3
                    if len(aa_line) - aa_mut_site >= frm_length :
                        aa_line = aa_line[:aa_mut_site+frm_length]
                    if aa_mut_site + 1 >= frm_length :
                        aa_line = aa_line[aa_mut_site - frm_length + 1:]
                    print aa_line
                    print len(aa_line)
                    for frames in range(len(aa_line) - frm_length + 1) :
                        new_frame = aa_line[frames:frames+frm_length]
                        out_fi_list.append(ab_line)
                        out_fi_list.append(new_frame)
            elif match_sub :
                if ab_list[-1][2] == '-' :
                    nlc_mut_site = int(ab_list[3]) - int(match_sub.group(2))
                    aa_mut_site = (nlc_mut_site - int(ab_list[-1][0])) / 3
                    if len(aa_line) - aa_mut_site >= frm_length :
                        aa_line = aa_line[:aa_mut_site+frm_length]
                    if aa_mut_site + 1 >= frm_length :
                        aa_line = aa_line[aa_mut_site - frm_length + 1:]
                    print aa_line
                    print len(aa_line)
                    for frames in range(len(aa_line) - frm_length + 1) :
                        new_frame = aa_line[frames:frames+frm_length]
                        out_fi_list.append(ab_line)
                        out_fi_list.append(new_frame)
                else :
                    nlc_mut_site = int(match_sub.group(2)) - int(ab_list[2])
                    aa_mut_site = (nlc_mut_site - int(ab_list[-1][0])) / 3
                    if len(aa_line) - aa_mut_site >= frm_length :
                        aa_line = aa_line[:aa_mut_site+frm_length]
                    if aa_mut_site + 1 >= frm_length :
                        aa_line = aa_line[aa_mut_site - frm_length + 1:]
                    print aa_line
                    print len(aa_line)
                    for frames in range(len(aa_line) - frm_length + 1) :
                        new_frame = aa_line[frames:frames+frm_length]
                        out_fi_list.append(ab_line)
                        out_fi_list.append(new_frame)
            elif match_ins :
                if ab_list[-1][2] == '-' :
                    nlc_mut_site = int(ab_list[3]) - int(match_ins.group(3))
                    aa_mut_site = (nlc_mut_site - int(ab_list[-1][0])) / 3
                    if len(aa_line) - aa_mut_site >= frm_length :
                        aa_line = aa_line[:aa_mut_site+frm_length]
                    if aa_mut_site + 1 >= frm_length :
                        aa_line = aa_line[aa_mut_site - frm_length + 1:]
                    print aa_line
                    print len(aa_line)
                    for frames in range(len(aa_line) - frm_length + 1) :
                        new_frame = aa_line[frames:frames+frm_length]
                        out_fi_list.append(ab_line)
                        out_fi_list.append(new_frame)
                else :
                    nlc_mut_site = int(match_ins.group(3)) - int(ab_list[2])
                    aa_mut_site = (nlc_mut_site - int(ab_list[-1][0])) / 3
                    if len(aa_line) - aa_mut_site >= frm_length :
                        aa_line = aa_line[:aa_mut_site+frm_length]
                    if aa_mut_site + 1 >= frm_length :
                        aa_line = aa_line[aa_mut_site - frm_length + 1:]
                    print aa_line
                    print len(aa_line)
                    for frames in range(len(aa_line) - frm_length + 1) :
                        new_frame = aa_line[frames:frames+frm_length]
                        out_fi_list.append(ab_line)
                        out_fi_list.append(new_frame)
    out_fi.write('\n'.join(out_fi_list)+'\n')            
    out_fi.close()
    in_mut.close()