Documentation read from 04/17/2019 22:07:27 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_reaction_description.

svr_reaction_description [-r ReactionID] [-c Column]

svr_reaction_description [-r ReactionID] [-c Column]

This simple utility gives the reaction associated with reaction IDs.



    svr_reaction_description -r rxn02270

would produce a single line containing a text expansion of the reaction, while

    svr_reaction_description -c 2 < tab.delimited.table > with.added.description

would take as input a table in which the second column contains reaction IDs, and an extra column is added to the output.


The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain a reaction ID.

If some other column contains the reaction IDs, use

    -c N

where N is the column (from 1) that contains the reaction IDs.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Command-Line Options

-c N

Specifies which column in the input table that contains the reaction IDs. Defaults to the last column in the input file.

-r reactionID

If specified, then the specified reaction ID will be used instead of reading the IDs from the input stream.


If specified, then the roles that trigger the reaction will be added to the output in additional columns after the reaction string.


If specified, then the compound names will be used in the reaction strings in addition to the compound IDs.


If specified, then the compound names will be used instead of the compound IDs in the reaction strings. This option overrides -n.

Output Format

The standard output is a tab-delimited file. Each line will contain the input fields followed by a description of the reaction. If -o is specified, then there will be an additional column for each role that triggers the reaction.