https://github.com/fhcrc/seqmagick

An imagemagick-like frontend to Biopython SeqIO
https://github.com/fhcrc/seqmagick

Last synced: 1 day ago
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An imagemagick-like frontend to Biopython SeqIO

• Host: GitHub
• URL: https://github.com/fhcrc/seqmagick
• Owner: fhcrc
• License: gpl-3.0
• Created: 2010-11-24T00:48:23.000Z (almost 14 years ago)
• Default Branch: master
• Last Pushed: 2024-03-18T15:45:02.000Z (8 months ago)
• Last Synced: 2024-10-03T00:39:35.839Z (about 1 month ago)
• Language: Python
• Homepage: http://seqmagick.readthedocs.org
• Size: 2.25 MB
• Stars: 112
• Watchers: 12
• Forks: 22
• Open Issues: 16
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGELOG.rst
  • License: LICENSE

Awesome Lists containing this project

• Awesome-Bioinformatics - seqmagick - file format conversion in Biopython in a convenient way. [ [web](http://seqmagick.readthedocs.io) ] (Next Generation Sequencing / Sequence Processing)

README

        
=========

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 `_ about

  sequence files

* Subsetting sequence files by:

  - Position

  - ID

  - Deduplication

  - `more`_

* Filtering sequences by `quality score

  `_

* Trimming alignments to a `region of interest

  `_ 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