An imagemagick-like frontend to Biopython SeqIO
Python Shell
Latest commit 5c7b05b Sep 24, 2015 @crosenth crosenth Merge pull request #54 from fhcrc/pct_ambig
new pct-ambiguous switch plus test cases

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.