An imagemagick-like frontend to Biopython SeqIO
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Latest commit 5c7b05b Sep 23, 2015 @crosenth crosenth Merge pull request #54 from fhcrc/pct_ambig
new pct-ambiguous switch plus test cases
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docs Update convert_mogrify.rst Aug 7, 2015
examples Some test data Feb 29, 2012
logo a few more sample seqmagick logos, with a less cheesy wand Apr 6, 2011
seqmagick new pct-ambiguous switch plus test cases Aug 18, 2015
.gitignore mimicking linux head and tail commands. Apr 29, 2014
.travis.yml Test against pypy Feb 13, 2013
CHANGELOG merge with master Sep 23, 2015
CONTRIB Update contrib Oct 10, 2013
INSTALL Update INSTALL with BioPython dependency May 18, 2011
LICENSE Restructure package Apr 7, 2011
MANIFEST.in Add manifest, test data Oct 5, 2012
README.rest
bump_version.sh Bump version for dev Jan 30, 2013
distribute_setup.py Use setuptools for installation Sep 14, 2011
doc-requirements.txt Replace program output plugin with hard text. Jul 14, 2015
seqmagick.py Use setuptools for installation Sep 14, 2011
setup.py Configure setuptools for nose tests. Fixes #55. Sep 2, 2015
tox.ini Happy colored tox tests Apr 30, 2014

README.rest

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

Features include:

  • 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.