all_entities_Contig
Return all instances of the Contig entity.
A contig is thought of as composing a part of the DNA associated with a specific genome. It is represented as an ID (including the genome ID) and a ContigSequence. We do not think of strings of DNA from, say, a metgenomic sample as "contigs", since there is no associated genome (these would be considered ContigSequences). This use of the term "ContigSequence", rather than just "DNA sequence", may turn out to be a bad idea. For now, you should just realize that a Contig has an associated genome, but a ContigSequence does not.
Example:
all_entities_Contig -a would retrieve all entities of type Contig and include all fields in the entities in the output.
Related entities
The Contig entity has the following relationship links:
- HasAsSequence ContigSequence
- HasVariationIn ObservationalUnit
- IsComponentOf Genome
- IsImpactedBy Trait
- IsLocusFor Feature
- IsSummarizedBy AlleleFrequency
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:
- source_id
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.