Return all instances of the Family entity.
The Kbase will support the maintenance of protein families (as sets of Features with associated translations). We are initially only supporting the notion of a family as composed of a set of isofunctional homologs. That is, the families we initially support should be thought of as containing protein-encoding genes whose associated sequences all implement the same function (we do understand that the notion of "function" is somewhat ambiguous, so let us sweep this under the rug by calling a functional role a "primitive concept"). We currently support families in which the members are translations of features, and we think of Features as having an associated function. Identical protein sequences as products of translating distinct genes may or may not have identical functions, and we allow multiple members of the same Family to share identical protein sequences. This may be justified, since in a very, very, very few cases identical proteins do, in fact, have distinct functions. We would prefer to reach the point where our Families are sets of protein sequence, rather than sets of protein-encoding Features.
Example:
all_entities_Family -a
would retrieve all entities of type Family and include all fields in the entities in the output.
The Family entity has the following relationship links:
Return all fields.
Display a list of the fields available for use.
Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:
The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. 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.