Robert Olson


A "location" is a sequence of "regions". A region is a contiguous set of bases in a contig. We work with locations in both the string form and as structures. fids_to_locations takes as input a list of fids. For each fid, a structured location is returned. The location is a list of regions; a region is given as a pointer to a list containing

             the contig,
             the beginning base in the contig (from 1).
             the strand (+ or -), and
             the length

Note that specifying a region using these 4 values allows you to represent a single base-pair region on either strand unambiguously (which giving begin/end pairs does not achieve).


    fids_to_locations [arguments] < input > output

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 identifer. If another column contains the identifier use

    -c N

where N is the column (from 1) that contains the subsystem.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Documentation for underlying call

This script is a wrapper for the CDMI-API call fids_to_locations. It is documented as follows:

  $return = $obj->fids_to_locations($fids)
Parameter and return types
$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a location
fids is a reference to a list where each element is a fid
fid is a string
location is a reference to a list where each element is a region_of_dna
region_of_dna is a reference to a list containing 4 items:
	0: a contig
	1: a begin
	2: a strand
	3: a length
contig is a string
begin is an int
strand is a string
length is an int

Command-Line Options

-c Column

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

-i InputFile [ use InputFile, rather than stdin ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added.

Input lines that cannot be extended are written to stderr.