[EMBOSS] Bug in degapseq ?

[Peter Rice]

Charles Plessy wrote:
> If I use degaspeq on a file, it prompts me for the name of the output, but if
> the data comes from stdin, degaspeq crashes. It does not happen if the name of
> the output is given.

> chouca〔~〕$ cat toto | degapseq stdin
> Removes gap characters from sequences
> output sequence(s) [xenopus-1a.fasta]: 
>    EMBOSS An error in ajmess.c at line 1662:
> END-OF-FILE reading from user

This is because you are reading from stdin, but then degapseq tries to 
read the output filename from stdin.

You do need to specify the output filename, or use -auto to accept the 
default (or -filter to use stdout and to read from stdin).

With -auto and -filter the program will no longer be using stdin for 
user replies.

Hmmm ... maybe we could catch these cases ... tricky though as really it 
is an explicit search for "stdin" as an input file/sequence. I could 
invent examples where we would guess wrongly.

Hope that helps,

Peter