[BioRuby] Clustal ALN writer

[Pjotr Prins]

On Wed, Jan 06, 2010 at 12:31:25PM +0900, Naohisa GOTO wrote:
> > How do you suppose we can do this so I can generate the ALN with
> > multiple match lines?
> 
> I'm afraid this is not regarded as Clustal format.
> Of course, it is technically easy to add such function.
> 
> There may be many private extensions of Clustal format.
> I think this is OK because Clustal format is rough,
> although this makes hard to validate Clustal format.

Standards are vague. EMBOSS does not even mention the match line, but
as ClustalW generates it we assume it is a 'standard'. I think most
parsers basically ignore lines starting with white space. So multiple
'match lines' should normally work. Many standards in bioinformatics
evolve from use - maybe my idea will become a standard one day ;-).

I think it is a nice feature to have. I'll add a warning that one
should use it with caution.

BTW the ALN-writer should really live in its own class/module, similar
to the current layout for the 'Report' class (which in reality is an
ALN parser, or ALN-reader). It is no surprise I did not find either of
them when I was looking for an implementation.

OK, I'll cook something up in a separate git branch.

Pj.