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revision 1.4, Tue Aug 10 01:10:05 2004 UTC revision 1.5, Thu Feb 16 22:03:22 2006 UTC
# Line 455  Line 455 
455  that pass a test.  The test is given by the command line arguments.  If the command line contains a single  that pass a test.  The test is given by the command line arguments.  If the command line contains a single
456  argument, it should be a file containing genome ids.  In the case, the test amounts to "keep PEGs from  argument, it should be a file containing genome ids.  In the case, the test amounts to "keep PEGs from
457  genomes corresponding to those in the given file".  If the command line arguments are of the form  genomes corresponding to those in the given file".  If the command line arguments are of the form
458  <i>-v File</>, then the test amounts to "keep only PEG ids from genomes other than those in the given file".  <i>-v File</i>, then the test amounts to "keep only PEG ids from genomes other than those in the given file".
459    
460  <li><b>step 4</b>: Now that we have a file on known machinery in genomes that probably do not have the original  <li><b>step 4</b>: Now that we have a file on known machinery in genomes that probably do not have the original
461  form of the enzyme, we use  form of the enzyme, we use

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