A Short Note on Mapping PEGs to Subsystems

A Short Note on Mapping PEGs to Subsystems

You can use

 svr_all_features 83333.1 peg | svr_ids_to_subsystems 2> /dev/null > E.coli.pegs.in.subsystems

to get a 2-column file [PEG,Subsystem] for the PEGs in the genome with ID 83333.1
(which happens to be E.coli).  If you also want the function of the PEGs, use

 svr_all_features 83333.1 peg | svr_ids_to_subsystems 2> /dev/null | svr_function_of -c 1 > E.coli.pegs.in.subsystems


The 

    svr_function_of -c 1

command takes as input a file in which each line is a tab-separated set of fields.  The

-c 1

says that the PEG ids for which functions are to be appended occur in the first column.

This produces output like

fig|83333.1.peg.2       CBSS-216591.1.peg.168   Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
fig|83333.1.peg.2       Lysine Biosynthesis DAP Pathway Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
fig|83333.1.peg.2       Threonine and Homoserine Biosynthesis   Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
fig|83333.1.peg.2       Threonine and Homoserine Biosynthesis   Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
fig|83333.1.peg.2       Methionine Biosynthesis Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
fig|83333.1.peg.3       Threonine and Homoserine Biosynthesis   Homoserine kinase (EC 2.7.1.39)
fig|83333.1.peg.3       Methionine Biosynthesis Homoserine kinase (EC 2.7.1.39)
fig|83333.1.peg.3       CBSS-269482.1.peg.1294  Homoserine kinase (EC 2.7.1.39)
fig|83333.1.peg.4       Threonine and Homoserine Biosynthesis   Threonine synthase (EC 4.2.3.1)
fig|83333.1.peg.6       YaaA    UPF0246 protein YaaA