region_to_fids

This command is used to take positions in contigs and to find fids that ocur within a specified distance of each position. It differs from locations_to_fids in which locations (list of regions) are explicitly given.

Example:

region_to_fids -d 10000 < input > output [gets fids within 10kb of the positions]

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 position. If another column contains the positions use

-c N

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

Positions are represented as Contig_Pos or Contig_Pos+1.

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 region_to_fids. It is documented as follows:

Parameter and return types

$region_of_dna is a region_of_dna
$return is a fids
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
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 position is not the last column.

-i InputFile [ use InputFile, rather than stdin ]

-d Distance [ all fids that are within this distance will be reported ]

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.