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=========
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
============
* Python >= 3.5
* biopython >= 1.78
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
========
* Modifying sequences: Remove gaps, reverse complement, reverse, change case,
- Remove gaps
- Reverse & reverse complement
- Trim to a range of residues
- Change case
- Sort by length or ID
- `more`_
* Displaying `information <http://seqmagick.readthedocs.org/en/latest/info.html>`_ about
sequence files
* Subsetting sequence files by:
- Position
- ID
- Deduplication
- `more`_
* Filtering sequences by `quality score
<http://seqmagick.readthedocs.org/en/latest/quality_filter.html>`_
* Trimming alignments to a `region of interest
<http://seqmagick.readthedocs.org/en/latest/primer_trim.html>`_ defined by the
forward and reverse primers
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
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