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revision 1.2, Fri Dec 11 21:52:20 2009 UTC revision 1.3, Tue Jul 13 18:34:27 2010 UTC
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17  the specified subsystems.  the specified subsystems.
18    
19  If you have a file with tab-delimited fields in which the last field  If you have a file with tab-delimited fields in which the last field
20  in each line is a functional role, then  in each line is a functional assignment, then
21    
22      svr_metabolic_reconstruction < file > extended.file      svr_metabolic_reconstruction < file > extended.file
23    
24  will produce a file in which each line contains a functional role that  will produce a file in which each line contains a functional role that
25  is part of an active subsystem.  For each such line, two extra  is part of an active subsystem.  Note that because each functional assignment
26  columns, the variant code and the subsystem, will be added.  Input  can contain multiple functional roles, a single incoming assignment can produce
27  lines corresponding to functional roles not placed in active  many such lines. For each such line, two extra columns, the variant code and the
28  subsystems will be written to STDERR (and will not appear in STDOUT).  subsystem, will be added. Input lines corresponding to functional roles not
29    placed in active subsystems will be written to STDERR (and will not appear in
30    STDOUT).
31    
32  Thus, if one had a FASTA file of protein sequences from some complete  Thus, if one had a FASTA file of protein sequences from some complete
33  genome or environmental sample, then  genome or environmental sample, then

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