for i in range (1,500):
    gaps = write_jc_matrices()
    stretch_cmd="../../../emboss/stretcher -datafile DNAMM -gapopen "+str(gaps[0])+" -gapextend "+str(gaps[1])+" -asequence seqa.fasta -bsequence seqb.fasta"
    (stretcher_in,stretcher_out) = os.popen4(stretch_cmd,"w")
    stretcher_in.write("\n\n")
    para2_cmd="../source/para2 -asequence seqa.fasta -bsequence seqb.fasta"
    (para2_in,para2_out) = os.popen4(para2_cmd,"w")
    para2_in.write("\n\n\n")
    time.sleep(1)
    para2_in.write("\n\n\n")
    #read in output
    #stretcher first:
    stretcher_file_out = open("seq.stretcher","r")
    stretcher_output = stretcher_file_out.read()
    #para2:
    para2_output = para2_out.readlines()
    print para2_output
    #cleanup
    stretcher_in.close()
    stretcher_out.close()
    stretcher_file_out.close()
    para2_in.close()
    para2_out.close()