svr_location_of

Get physical locations of genes.

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Example:

    svr_all_features 3702.1 peg | svr_location_of

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 locations of 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 ID of the feature for which locations are being requested. If some other column contains the feature IDs, 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.

-bounds

Normally, the location is returned as a comma-delimited list of location strings (each containing a contig ID, a start location, a strand indicator, and a length). Normally this would be a single location string, but some genes have multiple contiguous segments, and each segment is a separate string. If this option is specified, then only a single location-- one that covers all segments of the gene-- is output.

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added (the location associated with the feature).