locations_to_fids

It is frequently the case that one wishes to look up the genes that occur in a given region of a contig. Location_to_fids can be used to extract such sets of genes for each region in the input set of regions. We define a gene as "occuring" in a region if the location of the gene overlaps the designated region.

This command takes as input a table in which one column is a location. It adds an extra column which will contain a feature that overlaps the location. if n features overlap a location, then that input line will generate n output lines (each with an extra column giving one of the overlapping fids).

Example:

    locations_to_fids [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 location. If another column contains the location use

    -c N

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

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 locations_to_fids. It is documented as follows:

  $return = $obj->locations_to_fids($region_of_dna_strings)

Parameter and return types

$region_of_dna_strings is a region_of_dna_strings
$return is a reference to a hash where the key is a region_of_dna_string and the value is a fids
region_of_dna_strings is a reference to a list where each element is a region_of_dna_string
region_of_dna_string is a string
fids is a reference to a list where each element is a fid
fid is a string

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 an extra column (an overlapping fid) added.

Input lines that cannot be extended are written to stderr.