#format python

"""ReverseComplement using largely one reading 
"""

import sys

class Sequence:
    def __init__(self, seq='', name=''):
        self._seq = seq
        self._name = name
    def get_seq(self):
        return self._seq
    def get_name(self):
        return self._name


def Read_fasta(filename):
    file = open(filename, 'r')
    sequence = ''
    seq_tot = []      # sequence and name is saved in list data
    name = []
    while 1:
        line = file.readline()
        line = line.rstrip()
        if not line:
            break
        if line[0] == '>':
            name.append(line[1:])
            line = ''
            seq_tot.append(sequence)
            sequence = ''              # For another sequence reading
        sequence = sequence + line
        sequence.upper()
    seq_tot.append(sequence)
    del seq_tot[0]                     # At first time, delete first empty item
    return Sequence(seq_tot, name)


def trDnaCompl(seqclass):
    DnaCompl = {'A':'T', 'T':'A', 'G':'C', 'C':'G'}
    trname = seqclass.get_name()
    seq = seqclass.get_seq()
    trseq = []
    for sequence in seq:
        y = ''
        for back in range(len(sequence)-1, -1, -1):
            y = y + DnaCompl[sequence[back]]
        trseq.append(y)
    return Sequence(trseq, trname)


def Write_fasta(seqclass, wfile):
    names = seqclass.get_name()
    seqs = seqclass.get_seq()
    file = open(wfile, 'w')
    i = 0
    for name in names:
        file.write('>'); file.write(name)
        file.write('_reverse_complenent\n')
        seqseq = seqs[i]
        j = 0
        while seqseq[j:j+1] != '':
            seqline = seqseq[j:j+60]
            file.write(seqline); file.write('\n')
            j = j + 60
            
        i = i + 1
    file.close


def main(rfile, wfile):
    read = Read_fasta(rfile)       # Reading function
    trdna = trDnaCompl(read)       # Reverse Complement conversion function
    Write_fasta(trdna, wfile)      # Writing script


if __name__ == '__main__':
    rfile, wfile = sys.argv[1:3]
    main(rfile, wfile)