Ms-Fasta 0.1.0 (initial release)

[Simon Chiang]

Just released a module for working with FASTA files. At present the
library is really simple, basically an ExternalArchive to read the
FASTA format and a couple of tasks for loading data into a workflow.

% tap run -- load/fasta <fasta file> --range 1..10
% tap run -- load/random_fasta <fasta_file> --n 10

[Simon Chiang]

A link would be helpful... http://mspire.rubyforge.org/projects/ms-fasta/

[John Prince]

Simon,

I was hoping you would implement this with external :)

It looks great.

I've been looking at the bioruby Bio::FastaFormat API (http://bioruby.org/rdoc/classes/Bio/FastaFormat.html) and thinking that we should probably support the :seq method call, maybe with a method alias:

alias_method :seq, :sequence   # Bio uses :seq to return the sequence as a string

Its a little disturbing, but I can't seem to find a method that just returns the original header in FastaFormat...  there's nothing equivalent to :header in bioruby that I can find! [there really should be a way to get at the original header string, eh?]  Down the road we could probably use some of the Bioruby code to offer some nice functionality (http://bioruby.org/rdoc/classes/Bio/FastaDefline.html).

--John

[Simon Chiang]

I was hoping you would implement this with external :)

Yeah, it's funny... this is a bit of code I've had sitting around a while in a dusty bioactive project.  Accessing FASTA was the original reason I made external :)  

Down the road we could probably use some of the Bioruby code to offer some nice functionality (http://bioruby.org/rdoc/classes/Bio/FastaDefline.html).

Very cool!  We should definitely add that in, and the seq alias (maybe in a shim file?).