ous_with_trait

Example:

ous_with_trait -g Genome -mtype MeasurementType -min MinVal -max MaxVal < traits_input > output_with_ous

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 ous_with_trait. It is documented as follows:

Parameter and return types

$genome is a genome
$trait is a trait
$measurement_type is a measurement_type
$min_value is a float
$max_value is a float
$return is a reference to a list where each element is a reference to a list containing 2 items:
	0: an ou
	1: a measurement_value
genome is a string
trait is a string
measurement_type is a string
ou is a string
measurement_value is a float

Command-Line Options

-c Column

This is used only if the column containing the identifier is not the last column.

-g genome [ We are extracting ous for which this is the reference genome ]

-i InputFile [ use InputFile, rather than stdin ]

-mtype Type [ Measurement Type ]

-min MinVal [ Minimum value of measurement ]

-max MaxVale [ maximum value of measurement ]

Output Format

The standard output is a tab-delimited file. It consists of the input file with extra columns added (the measurement vlue and an ou with that value).

Input lines that cannot be extended are written to stderr.