get_entity_ContigSequence

ContigSequences are strings of DNA. Contigs have an associated genome, but ContigSequences do not.. We can think of random samples of DNA as a set of ContigSequences. There are no length constraints imposed on ContigSequences -- they can be either very short or very long. The basic unit of data that is moved to/from the database is the ContigChunk, from which ContigSequences are formed. The key of a ContigSequence is the sequence's MD5 identifier.

Example:

get_entity_ContigSequence -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 ContigSequence entity has the following relationship links:

HasSection ContigChunk

IsSequenceOf Contig

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:

length

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.