[bip] welcome!

[Andrew Dalke]

On Aug 1, 2007, at 4:08 AM, Bruce Southey wrote:
> I know! I was surprised when I first found out about it.
>
> The main source that I can find is the file FASTA.doc which is the
> documentation for 'The FASTA program package' . So I am not sure if
> you can get much more 'authoritative' than that.

Huh.  How did I miss that?  Ah, I probably forgot that ".doc"
once upon a time had a less strong association with Word.
Yes, that documentation is included with the FASTA source
distribution.

> Consequently, every
> package or reference that ignores the comment line is not implementing
> the full FASTA spec and should be treated as such.

Effectively that's every single package and reference.

Treated how?  With disdain?  Or lots of love and TLC?  :)

No databases and no programs support it.  It's a non-issue.
It can never change.  There's too much installed base
that will break if a database is released in that format.
And with no databases in that format, no one will write
the parsers for it.

You don't like my justification that everyone supports
the NCBI FASTA file format, rather than the Pearson one?


The FASTA algorithm parses a (slightly different) file
format than the spec describes.  I think it allows the
sequence and comment lines to intermix.

>          if (line[0]!='>'&& line[0]!=';') {
>            for (i=0; (n<maxs && rn < sstop)&&
>                   ((ic=qascii[line[i]&AAMASK])<EL); i++)
>              if (ic<NA && ++rn > sstart ) seq[n++]= ic;
>            if (ic == ES || rn > sstop) break;
>          }

If this is correct, does this mean that FASTA does
not implement the full FASTA spec?

BioJava does not support ;comments.
BioPython does not support them either.

I could check Emboss, and BioRuby, and .. ooh!  Lisp
code to read FASTA files:
   http://nostoc.stanford.edu/Docs/iteration.html

Nope, no comments there.

It's a dead issue.  This comment is no more! He has ceased
to be! He's expired and gone to meet his maker!
   http://www.mtholyoke.edu/~ebarnes/python/dead-parrot.htm
  ;)



				Andrew
				dalke at dalkescientific.com