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



Takes as input a table containing reaction IDs and adds 2 columns giving the distance and the connected reaction.

------ Example: svr_all_reactions | svr_neighboring_reactions -d 2 > table.with.neighboring.reactions

would produce a 3-column table: [reactionID1,Distance,ReactionID2]

         svr_neighboring_reactions -r rxn09225

would produce a 3-column table in which each line represents a reaction connected (immediately connected, since -d defaults to 1) to rxn09225.


Command-Line Options

-c Column

This is used only if the column containing reaction IDs is not the last.

-d MaxDist [default=1]

Gives the maximum distance. The computation becomes extremely expensive as this value goes up.

-r Reaction

Gives a single reaction, rather than taking reactions from an input file.

Output Format

The standard output is a tab-delimited file. It consists of the input file with two extra columns (distance and connected reaction).


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