all_entities_ContigChunk
Return all instances of the ContigChunk entity.
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:
all_entities_ContigChunk -a would retrieve all entities of type ContigChunk and include all fields in the entities in the output.
Related entities
The ContigChunk entity has the following relationship links:
Command-Line Options
- -a
-
Return all fields.
- -h
-
Display a list of the fields available for use.
- -fields field-list
-
Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:
- sequence
Output Format
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.