query_entity_Contig
Query the entity Contig.
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:
query_entity_Contig -a 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
- -is field,value
-
Limit the results to entities where the given field has the given value.
- -like field,value
-
Limit the results to entities where the given field is LIKE (in the sql sense) the given value.
- -op operator,field,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.
- -a
-
Return all fields.
- -h
-
Display a list of the fields available for use.
- -fields field-list
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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 containing a column for each requested field.