[EMBOSS] Re: input file names
Peter Rice
pmr at ebi.ac.uk
Wed Nov 24 08:57:42 UTC 2004
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
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