[EMBOSS] Re: input file names

[Peter Rice]

Julian Mintseris wrote to emboss-bug:

> Dear EMBOSS,
> 
> I realize that this is not really a bug:
> 
> EMBOSS programs (such as water) do not like input filenames containing
> colons.
> 
> Of course I could just rename my files, but if there is another simple
> workaround, I would appreciate it if you let me know.

For filenames themselves, there is a possible workaround...

If the part before the : is not a database - and we do have rules for database 
names - or for :: if it is not a valid format, we could try to look for an 
existing file with that name.

For output files, sorry - we would have to object that the format (no database 
names on output - yet) is not valid, rather than using the string as a new 
filename.

This means EMBOSS would not be able to create sequence files with such names. 
We will possibly be using a "format:" syntax for other input and output files 
in the near future as it is a nice clean way

Hope this helps. I have copied this to the emboss mailing list in case the 
topic is of more general interest.

Peter