Skip to main content
Warning: You are using the test version of PyPI. This is a pre-production deployment of Warehouse. Changes made here affect the production instance of TestPyPI (testpypi.python.org).
Help us improve Python packaging - Donate today!

Fast Stockholm to other formats Multiple Sequence Alignment reformater.

Project Description
====
stockholm_reformat
====

Fast Stockholm to other formats Multiple Sequence Alignment reformater.

Includes an API and a command line script. The pure Python version is already several times faster than the
Perl script contained in the `MPI Bioinformatics Toolkit. <http://toolkit.tuebingen.mpg.de/reformat/help_param>`_

The following outuput supported formats are:

* a3m
* fasta
* aln

Usage
----
From Python::

stockholm_reformat.parse_a3m('inputfile.sto', 'outputfile.a3m')
stockholm_reformat.parse_fasta('inputfile.sto', 'outputfile.fasta')
stockholm_reformat.parse_aln('inputfile.sto', 'outputfile.aln')

If you have a working C compiler, you may have the compiled versions installed::

stockholm_reformat.cparse_a3m('inputfile.sto', 'outputfile.a3m')
stockholm_reformat.cparse_fasta('inputfile.sto', 'outputfile.fasta')
stockholm_reformat.cparse_aln('inputfile.sto', 'outputfile.aln')

They are around twice as fast.

Both input and output can be provided as file names or file handles.

From the command line::

$ stockholm_to_a3m input.sto output.a3m
$ stockholm_to_fasta input.sto output.fasta
$ stockholm_to_aln input.sto output.aln
Release History

Release History

This version
History Node

0.3.1

History Node

0.3

History Node

0.2

History Node

0.1

Download Files

Download Files

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

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
stockholm_reformat-0.3.1.tar.gz (53.5 kB) Copy SHA256 Checksum SHA256 Source Nov 17, 2016

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting