svr_reaction_description [-r ReactionID] [-c Column]

This simple utility gives the reaction associated with reaction IDs.

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Examples:

    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.

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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.

-o

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

-n

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

-f

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.