get_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:

get_entity_Contig -a < ids > table.with.fields.added

would read in a file of ids and add a column for each filed in the entity.

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the id. If some other column contains the id, use

-c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the output is to the standard 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

-c Column

Use the specified column to define the id of the entity to retrieve.

-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.