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.

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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 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.

-v

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.

-escape

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.

clearinghouse_register_subsystem_id

    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.

ss_name

Full name of the relevant subsystem.

RETURN

Short ID of the subsystem.