.. 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
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
Modifying sequences: Remove gaps, reverse complement, reverse, change case,
more
_Displaying information <http://seqmagick.readthedocs.org/en/latest/info.html>
_ about
sequence files
Subsetting sequence files by:
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