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.
This script is a wrapper for the CDMI-API call ous_with_trait. It is documented as follows:
$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
This is used only if the column containing the identifier is not the last column.
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.
To install Bio::KBase, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::KBase
CPAN shell
perl -MCPAN -e shell install Bio::KBase
For more information on module installation, please visit the detailed CPAN module installation guide.