get_relationship_IsLocusFor

A feature is a set of DNA sequence fragments. Most features are a single contiquous fragment, so they are located in only one DNA sequence; however, fragments have a maximum length, so even a single contiguous feature may participate in this relationship multiple times. A few features belong to multiple DNA sequences. In that case, however, all the DNA sequences belong to the same genome. A DNA sequence itself will frequently have thousands of features connected to it.

Example:

get_relationship_IsLocusFor -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 Feature entity to return. Field-list is a comma-separated list of strings. The following fields are available:

id

feature_type

source_id

sequence_length

function

alias

-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

ordinal

begin

len

dir

-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.