fhcrc / seqmagick

An imagemagick-like frontend to Biopython SeqIO
http://seqmagick.readthedocs.org
GNU General Public License v3.0
113 stars 22 forks source link

========= seqmagick

.. image:: https://travis-ci.org/fhcrc/seqmagick.svg?branch=master :target: https://travis-ci.org/fhcrc/seqmagick

We often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. seqmagick is a kickass little utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments::

seqmagick convert a.fasta b.phy    # convert from fasta to phylip
seqmagick mogrify --ungap a.fasta  # remove all gaps from a.fasta, in place
seqmagick info *.{fasta,sto}       # describe all FASTA and Stockholm
                                   # files in the current directory

Requirements

Installation

Use pip::

pip install seqmagick

Note that as of version 0.8.0, this package requires Python 3.5+. If you want to use the most recent version compatible with Python 2.7::

pip install seqmagick==0.6.2

Features

Want to learn more? Head to the Documentation_.

seqmagick is free software under the GPL v3.

.. _Documentation: http://seqmagick.readthedocs.org/en/latest/

.. _more: http://seqmagick.readthedocs.org/en/latest/convert_mogrify.html