svr_metabolic_reconstruction

Get a metabolic reconstruction from a set of functional roles.

By a metabolic reconstruction we mean a detailed list of subsystems that we believe are present in a genome or environmental sample, along with the specific variant codes that are attached to occurrences of the specified subsystems.

If you have a file with tab-delimited fields in which the last field in each line is a functional assignment, then

    svr_metabolic_reconstruction < file > extended.file

will produce a file in which each line contains a functional role that is part of an active subsystem. Note that because each functional assignment can contain multiple functional roles, a single incoming assignment can produce many such lines. For each such line, two extra columns, the variant code and the subsystem, will be added. Input lines corresponding to functional roles not placed in active subsystems will be written to STDERR (and will not appear in STDOUT).

Thus, if one had a FASTA file of protein sequences from some complete genome or environmental sample, then

    svr_assign_using_figfams < ProteinSequences | svr_metabolic_reconstruction > reconstruction 2> unplaced.hits

would give you the assignments of function plus the unplaced sequences.