locations_to_dna_sequences

locations_to_dna_sequences takes as input a list of locations (each in the form of a list of regions). The routine constructs 2-tuples composed of

     [the input location,the dna string]

The returned DNA string is formed by concatenating the DNA for each of the regions that make up the location.

Example:

    locations_to_dna_sequences [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 locations_to_dna_sequences. It is documented as follows:

  $dna_seqs = $obj->locations_to_dna_sequences($locations)

Parameter and return types

$locations is a locations
$dna_seqs is a reference to a list where each element is a reference to a list containing 2 items:
	0: a location
	1: a dna
locations is a reference to a list where each element is a location
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
dna 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 extra columns added.

Input lines that cannot be extended are written to stderr.