[EMBOSS] emboss stand-in for fasta

[Peter]

On Sat, Jul 24, 2010 at 11:56 AM, Ingo P. Korndoerfer
<korndoerfer at crelux.com> wrote:
> could anybody help me out with what to use as a stand-in for fasta ?
>
> fasta by itself is fine, but under windows there is no way to make fasta
> accept filenames with spaces.  neither "" nor """" nor '' seem to alleviate
> the problem.

You are talking about Bill Pearson's FASTA command line tools, right?
Have you tried wrapping the filename with double quote characters,
"like this.fasta", which usually works on Windows. If not, I'd also try
escaping with a slash, "like\ this.fasta", just in case.

> so i was hoping emboss would have something (which would also save
> me having to install fasta on all of our pcs).
>
> what i need to do is run a sequence against an in house library and
> return me the top hit in alignment.

Sounds like BLAST might we a sensible choice to me - it works fine
on Windows, although I'm not sure about filenames with spaces.

Personally I avoid filenames with spaces - they just cause trouble.
Can't you rename things before calling FASTA? e.g. Write a wrapper
script for FASTA to turn spaces into underscores?

Peter