alleles_to_traits

Example:

alleles_to_traits [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 identifier.

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 alleles_to_traits. It is documented as follows:

Parameter and return types

$alleles is an alleles
$return is a reference to a hash where the key is an allele and the value is a traits
alleles is a reference to a list where each element is an allele
allele is a string
traits is a reference to a list where each element is a trait
trait is a string

Command-Line Options

-c Column

This is used only if the column containing the identifier 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.