[EMBOSS] Bug in degapseq ?

[Peter Rice]

Charles Plessy wrote:

> Oh, I completely overlooked the fact that the emboss programs can take
> their user replies from stdin. Maybe then the most straightforward to
> inform users from this mistake would be to change the error message to
> something like : "Error: could not open file '...............', in which
> the name of the file would be truncated to the end of the line. The user
> would quickly understand if the file name is someting like AGTCCAGGTA...

Or perhaps they would not quickly understand ... because it took me a 
few runs before I realised that was the problem :-)

I think we can keep track of stdin being opened in EMBOSS and refuse to 
prompt for input.

regards,

Peter