svr_intergenic_regions

List all the intergenic regions in the contigs for a specified genome.

Intergenic regions are defined here as areas of the contig not occupied by features of specified types, usually PEG and/or RNA.

The genome ID and the types of features to be considered in computing the regions are specified on the command line. The output will be a flat file containing "Location Strings" in SAP, one per line. For example,

    svr_intergenic_regions 360108.3 peg rna

would output strings for the locations in the contigs for genome 360108.3 that are not used by PEGs or RNAs.

Command-Line Options

url

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

Output Format

The standard output is a file where each line just contains a location string.