[Biopython] seqmagick

[Connor McCoy]

Hi all,

We wrote (and use) seqmagick, a little tool to conveniently access
BioPython's Sequence I/O and manipulation capabilities from the command
line.

Seqmagick allows one to extract summary information on sequence files,
convert between formats based on file extension, modify sequences, and
much more. For example:

# Convert from fasta to stockholm
> seqmagick convert seqfile.fasta seqfile.sto

# Reverse complement the first 5 sequences in file
> seqmagick convert --reverse-complement --head 5 seqfile.fasta seqfile.rev=
comp.fasta

# Remove all columns containing > 5% gaps, in place
> seqmagick mogrify --squeeze-threshold 0.95 seqfile.fasta

For more info, see: http://fhcrc.github.com/seqmagick/

Or to install:

     pip install seqmagick

Comments / contributions welcome.

Cheers,
Connor