Incenp.Bioutils - Incenp.org’s utilities for computational biology
Incenp.Bioutils is a set of command line utilities and helper Python modules to deal with some computational biology tasks.
SeqTool is intended as a “Swiss Army knife” to perform various operations on biological sequence files.
Among other things, it provides wrappers for the
alignment tools; the main interest of those wrappers is that they can be
used with sequences in any format supported by Biopython’s SeqIO module,
whereas the original tools only read files in the FASTA format.
SeqVault is a command-line interface to BioSQL databases.
SeqVault is intended to be used with a slightly modified version of the
BioSQL database schema (provided in the
biosql directory), where every
biodatabase is associated with a 3-letters prefix. That prefix is then
used to automatically assign accession numbers (of the form
PRE is the prefix) when importing sequences into the database.
However SeqVault can also be used with pristine BioSQL databases.
Quickstart (example with PostgreSQL)
Create a new PostgreSQL user account and a new database::
# createuser <username> # createdb -O owner <username> <dbname>
Initialize the newly created database by running the provided
$ psql -h localhost -U <username> <dbname> < biosql/biosqldb-pg.sql
Next, create a plaintext file in
and fill it as follows::
[Server] host: localhost user: <username> password: <PostgreSQL user password> database: <dbname>
SeqVault is now ready to be used.
CC3d-Runner is a small wrapper around the command-line interface of CompuCell3D, to run headless simulations.
The main helper module is the
incenp.bio.seq.usa module, which
provides an implementation of the Uniform Sequence Address format
A Uniform Sequence Address or USA is a way to refer to a biological sequence and to fetch that sequence from its source.
The following example shows how to read a sequence specified by a USA::
from incenp.bio.seq import usa records = usa.read_usa('genbank::file.gb:acc:X65923')
records object is an array of
The following Python packages are necessary:
ReportLab is required to run the
subcommand of the
seqvault utility requires a SQL adapter for the database server
you plan to use it with, such as psycopg2 for
Incenp.Bioutils is distributed under the terms of the GNU General Public License, version 3 or higher. The full license is included in the COPYING file of the source distribution.