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Robert Olson > Bio-KBase-0.06 > scripts/reaction_strings


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reaction_strings ^

Reaction_strings are text strings that represent (albeit crudely) the details of Reactions.


    reaction_strings [arguments] < input > 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 another column contains the identifier use

    -c N

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

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

Documentation for underlying call

This script is a wrapper for the CDMI-API call reaction_strings. It is documented as follows:

  $return = $obj->reaction_strings($reactions, $name_parameter)
Parameter and return types
$reactions is a reactions
$name_parameter is a name_parameter
$return is a reference to a hash where the key is a reaction and the value is a string
reactions is a reference to a list where each element is a reaction
reaction is a string
name_parameter is a string

Command-Line Options

-c Column

This is used only if the column containing the subsystem is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column (the readable reaction string) added.

Input lines that cannot be extended are written to stderr.

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