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  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()