import sys

from altschulEriksonDinuclShuffle import *
            
def readFastaFile(infile,outfile):

    fin = open(infile)
    out = open(outfile,'w')
    
    currSeq=''
    currSeqname=None
    for line in fin:
        if '>' in line:
            if  currSeqname !=None:
                out.write(currSeqname+dinuclShuffle(currSeq)+'\n')
                currSeqname=None
                currSeq=''
            currSeqname=line
        else:
            currSeq=currSeq+line.strip().upper()

    if currSeqname!=None:
        out.write(currSeqname+dinuclShuffle(currSeq)+'\n')
    
    fin.close()
    out.close()

def readrawseq(infile,outfile):
    '''
    each line is a sequence
    '''
    fin = open(infile)
    out = open(outfile,'w')
    for line in fin:
        out.write(dinuclShuffle(line.strip().upper())+'\n')
    fin.close()
    out.close()
    
def main():
    seqfile = sys.argv[1]
    outfile = sys.argv[2]
    fasta = sys.argv[3]

    if fasta == 'fasta':
        readFastaFile(seqfile,outfile)
    else:
        readrawseq(seqfile,outfile)

main()