Hadoop reducer according an inout

[Daniel Yehdego <dt...@miners.utep.edu>]

Hi, 
I am using Hadoop streaming to distribute some biological data strings. My mapper is some executable binary program to determine the structure of a certain input. I am also using some reducer script to glue the output strings from the mapper so that I have a one long string. But I have a problem that the order of the output string is not same as the input from the mapper. Is there a way that I can use Hadoop so that the output is in the same order as the input.
Assume we have an output from the mapperMAP1<RNA-1><STRUCTURE-1>MAP2<RNA-2><STRUCTURE-2>MAP3<RNA-3><STRUCTURE-3>and what I am looking is to reduce in the following manner: <RNA-1><RNA-2><RNA-3>\t<STRUCTURE-1><STRUCTURE-2><STRUCTURE-3>\n
your input highly appreciated. Thanks in advance.Regards, 

Daniel T. Yehdego
Computational Science Program 
University of Texas at El Paso, UTEP 
dtyehdego@miners.utep.edu