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
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.
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
- -c Column
This is used only if the column containing the subsystem is not the last column.
- -i InputFile [ use InputFile, rather than stdin ]
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.