This is the home page of SeqVault, a command line tool to manage a repository of biological sequence data. It is mainly a thin wrapper around the BioSQL database schema and some of the Biopython modules.
SeqVault is distributed under the terms of the GNU General Public License, version 3 or higher.
You need a PostgreSQL
server (not necessarily on your machine, but it must be reachable
from your machine). Create a dedicated PostgreSQL user account
and a dedicated database for SeqVault, then initialize the
database by loading the provided
$ psql -h hostname -U username database < biosql/biosqldb-pg.sql
Create a file named
$XDG_CONFIG_HOME/seqvault/seqvault.rc with the
[Server] host: hostname user: username password: password database: database
Install the following Python modules: Psycopg2, Biopython, and IPython (this last one is optional).
SeqVault may now be used directly from the source directory, or
it may be installed as a Python package using the provided
svc program alone will list the
available subcommands. Calling
command will display the help for the specified
Here are the basics steps in using SeqVault:
$ svc db new vectors "Vectors database" VEC
This will create a new subdatabase called
sequences stored in this database will have an accession number
starting with the “VEC” prefix (so VEC_000000, VEC_000001, and so
$ svc add vectors sequence.gb
This will add the sequence(s) contained in the
sequence.gb to the previously created “vectors”
database. The command will also print the sequence(s) as stored
on the standard output.
Note that only GenBank-formatted files are accepted.
$ svc list vectors
This will list the sequences stored in the “vectors” subdatabase.
$ svc get VEC_000003
This retrieves the sequence(s) identified by the specified accession number(s). Sequences are printed on standard output.
$ svc edit VEC_000003
This will fire a text editor (currently gVim—this is not modifiable at runtime right now) loaded with the text of the specified sequence. After the editor is closed and if the sequence has been modified, the modified sequence will be stored back in the database.
The source code is available in a Git repository; clone it with the following command:
$ git clone https://git.incenp.org/damien/seqvault.git
No tarball distribution has been released yet, but you may download a snapshot of the “develop” branch.