Skip to main content

Python wrapper around libclustalo

Project description

This is just a simple Python wrapper around Clustal Omega (http://www.clustal.org/omega/), used internally at Benchling but casually open source, if it helps anybody. Also available via:

pip install clustalo

Requires libclustalo installed, version 1.2.0. On Linux, it’s recommended you build and install it yourself:

cd clustal-omega-1.2.0
./configure --with-pic --with-openmp
make && sudo make install

before installing this package.

Support for OSX is not quite there yet, mainly because OpenMP isn’t supported on clang. Homebrew is still on 1.1.0, so you’ll need to compile and install clustalo 1.2.0 yourself (–without-openmp). You’ll also need to modify the setup.py file to leave out gomp and -fopenmp when installing.

Usage

from clustalo import clustalo
input = {
    'seq1': 'AAATCGGAAA',
    'seq2': 'CGGA'
}
aligned = clustalo(input)
# aligned is a dict of aligned sequences:
#   seq1: AAATCGGAAA
#   seq2: ----CGGA--

At the moment, input sequences are assumed to not be aligned (i.e. there is no dealign option). See clustalo.clustalo.__doc__ or file clustaslo/clustalo.c for documentation.

Project details


Release history Release notifications

This version
History Node

0.1.1

History Node

0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
clustalo-0.1.1.macosx-10.9-x86_64.tar.gz (260.0 kB) Copy SHA256 hash SHA256 Dumb Binary 2.7 Jul 23, 2014
clustalo-0.1.1.tar.gz (3.0 kB) Copy SHA256 hash SHA256 Source None Jul 23, 2014

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page