svr_subsystem_spreadsheet

    svr_subsystem_spreadsheet "subsystem ID" >sub_data.tbl

Output a subsystem's spreadsheet.

This script takes as input a subsystem name on the command line and produces a tab-delimited file that organizes the features of the subsystem by genome and role. There will be one output line per genome. The first column will contain the genome ID, the second the relevant variant code, and then each other column will correspond to one of the subsystem's roles (effectively, a spreadsheet cell). The features performing the role in the subsystem will be placed in the appropriate position as a comma-delimited list.

Note that because the subsystem name likely contains spaces, it will need to be enclosed in quotes on the command-line.

Command-Line Options

url

The URL for the Sapling server, if it is to be different from the default.

aux

If specified, auxiliary roles will be included in the output. Normally these are excluded.