import string,os,sys,getopt


def usage():
    print """
    dnda_2d.py [OPTIONS]

    OPTIONS can be

        -h,--help       This message
        -f,--file       The file containing the base sequence
        -s,--stdin      Read the sequence from stdin
        -n,--nograph    Do'nt generate a graphical plot
    """
    
def make2drep(seq):
    currx = 0
    curry = 0
    points = []
    for base in seq:
        if base in [' ','\n']: continue

        if base in ['a','A']:
            currx += 1
        if base in ['t','T']:
            currx = currx - 1
        if base in ['c','C']:
            curry += 1
        if base in  ['g','G']:
            curry =curry - 1
        points.append( (currx,curry) )
    return(points)        
    
def main():

    seqfile = ''
    stdin = 0
    graph = 1
    
    if len(sys.argv) == 1:
        usage()
        sys.exit(0)

    try:
        opt,args = getopt.getopt(sys.argv[1:], 'hf:ns',\
        ['file=','nograph','help','stdin'])
    except getopt.GetoptError:
        usage()
        sys.exit(0)

    for o,a in opt:
        if o in ('-h','--help'):
            usage()
            sys.exit(0)
        if o in ('-f','--file'):
            seqfile = a
        if o in ('-n','--nograph'):
            graph = 0
        if o in ('-s','--stdin'):
            stdin = 1
    
    # Read in the sequence
    seq = ''
    if seqfile:
        try:
            f = open(seqfile,'r')
            for line in f:
                seq += line
            f.close()
        except IOError:
            print """
            Could'nt open %s
            """ % (seqfile)
            sys.exit(0)
    else:
        seq = sys.stdin.readline()
            
    # Make the 2D rep
    points = make2drep(seq)

    f = open('rep.dat','w')
    for x,y in points:
        f.write('%d %d\n' % (x,y))
    f.close()        

    if graph:
        # show a plot
        import StringIO,time

        s = StringIO.StringIO()
        s.write('set size square\n')
        s.write('set term png\n')
        s.write('set out \'rep.png\'\n')
        s.write('plot \'rep.dat\' title \'%s\' with lines\n' % (seqfile))
        s.write('set term x11\n')
        s.write('plot \'rep.dat\' title \'%s\' with lines\n' % (seqfile))

        o,i,e = os.popen3('gnuplot -persist')
        o.write(s.getvalue())
        o.close()
        time.sleep(1)

if __name__ == '__main__':
    main()