get_relationship_HasAsSequence

This relationship connects a Contig as it occurs in a genome to the Contig Sequence that represents the physical DNA base pairs. A contig sequence may represent many contigs, but each contig has only one sequence.

Example:

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

would read in a file of ids and add a column for each field in the relationship.

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.

Command-Line Options

-c Column

This is used only if the column containing id is not the last.

-from field-list

Choose a set of fields from the ContigSequence entity to return. Field-list is a comma-separated list of strings. The following fields are available:

id

length

-rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of strings. The following fields are available:

from_link

to_link

-to field-list

Choose a set of fields from the Contig entity to return. Field-list is a comma-separated list of strings. The following fields are available:

id

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.