Documentation read from 04/17/2019 22:07:26 version of /vol/public-pseed/FIGdisk/FIG/bin/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.


    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 with the -complete option).

Command-Line Options


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


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


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.


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.


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


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.