svr_get_all

Process a general query against the Sapling database.

This command performs a generalized query against the Sapling database using a path through the entities and relationships and a parameterized constraint. A list of output fields is used to produce a tab-delimited output file. The content of this file is completely variable, dependent entirely on the fields chosen.

For a description of how to create queries using this command, refer to "Queries" in ERDB and "GetAll" in ERDB to understand how queries work, and to the Sapling database documentation for a description of the entities, relationships, and fields in the database.

Examples

    svr_get_all -p 'Feature Produces ProteinSequence' -c 'Feature(id) = ?' -v 'fig|1247729.4.peg.1025' -f 'Feature(function),ProteinSequence(sequence)'

would produce a 2-column file with a single row. The first column would contain the functional assignment of the identified feature (fig|1247729.4.peg.1025) and the second its protein sequence.

    svr_get_all -p 'Genome IsOwnerOf Feature' -c 'Genome(scientific-name) LIKE ? AND Feature(feature-type) = ?' -v 'Campylobacter %,rna' -f 'Feature(id)'

would produce a 1-column file with multiple rows. The file would contain the IDs of all the RNA features in Campylobacter genomes.

    svr_get_all -p 'Genome' -c 'Genome(complete) = 1 ORDER BY Genome(scientific-name)' -f 'scientific-name,id'

would produce a 2-column file containing the name and ID of each complete genome, ordered by genome name. (Note that this is the same as the output from the command svr_all_genomes.pl with the -complete option).

Command-Line Options

url

The URL for the Sapling server, if it is to be different from the default.

p

The path through the Sapling database (see "Object Name List" in ERDB) for the query to follow.

c

The constraint (see "Filter Clause" in ERDB) for the query, expressed in a syntax similar to an SQL WHERE clause. Note that the LIMIT option is prohibited. Use the -n parameter of this command instead.

v

A comma-delimited list of the parameter values to be substituted into the constraint. There must be one parameter in this list for each question mark in the constraint.

f

A comma-delimited list of the names for the fields to return.

n

The maximum number of results to return. If omitted, all qualifying results will be returned.

Output Format

The standard output is a file where each line contains a genome name and a genome ID.