Query the entity ContigChunk.
ContigChunks are strings of DNA thought of as being a string in a 4-character alphabet with an associated ID. We allow a broader alphabet that includes U (for RNA) and the standard ambiguity characters. The notion of ContigChunk was introduced to avoid transferring/manipulating huge contigs to access small substrings. A ContigSequence is formed by concatenating a set of one or more ContigChunks. Thus, ContigChunks are the basic units moved from the database to memory. Their existence should be hidden from users in most circumstances (users are expected to request substrings of ContigSequences, and the Kbase software locates the appropriate ContigChunks).
Example:
query_entity_ContigChunk -a
The ContigChunk entity has the following relationship links:
Limit the results to entities where the given field has the given value.
Limit the results to entities where the given field is LIKE (in the sql sense) the given value.
Limit the results to entities where the given field is related to the given value based on the given operator.
The operators supported are as follows. We provide text based alternatives to the comparison operators so that extra quoting is not required to keep the command-line shell from confusing them with shell I/O redirection operators.
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 containing a column for each requested field.
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.