Example:
fids_to_feature_data [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.
This script is a wrapper for the CDMI-API call fids_to_feature_data. It is documented as follows:
$return = $obj->fids_to_feature_data($fids)
$fids is a fids $return is a reference to a hash where the key is a fid and the value is a feature_data fids is a reference to a list where each element is a fid fid is a string feature_data is a reference to a hash where the following keys are defined: feature_id has a value which is a fid genome_name has a value which is a string feature_function has a value which is a string feature_length has a value which is an int feature_publications has a value which is a pubrefs feature_location has a value which is a location pubrefs is a reference to a list where each element is a pubref pubref is a reference to a list containing 3 items: 0: a string 1: a string 2: a string 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
This is used only if the column containing the subsystem is not the last column.
The standard output is a tab-delimited file. It consists of the input file with extra columns added in this order:
Feature identifier
List of Pubmed identifiers for publications associated with this feature.
Name of the genome this feature is present in.
Location string describing the location of this feature in its genome.
Length of the DNA sequence of this feature.
The function currently assigned to this feature.
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.