Documentation read from 04/17/2019 22:07:25 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_evidence.



Get evidence codes for protein-encoding genes

------ Example: svr_all_features 3702.1 peg | svr_evidence

would produce a 2-column table. The first column would contain PEG IDs for genes occurring in genome 3702.1, and the second would contain the evidence codes (comma-separated) for those genes.


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 the PEG for which aliases are being requested. If some other column contains the PEGs, use

    -c N

where N is the column (from 1) that contains the PEG in each case.

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 Column

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


The verbose option will cause an english language version of the evidence to be returned in a column after the comma-separated list of evidence codes.


TRUE if the output text should be escaped for HTML, else FALSE

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (a comma-separated list of aliases), and, if the -v option is used, an extra column consisting of the english language version of the evidence.


    my $tax = FIGRules::clearinghouse_register_subsystem_id($ss_name);

Return a subsystem's short ID. Short IDs are maintained at a special clearinghouse web site. If the subsystem does not yet have a short ID, a new one will be assigned by the clearinghouse and returned.


Full name of the relevant subsystem.


Short ID of the subsystem.