Edgar Crowdy crowdy at
Fri May 9 14:57:37 UTC 2003

Claude Beazley wrote:
> I've noticed that most emboss apps that produce a sequence file use the -outseq parameter whereas coderet seems to use -seqout shouldn't this be kept consistant?

"seqout" is an ACD datatype, and codret is using a datatype name as a 
parameter name, which is probably not a great idea. But, as much as I'm 
all for consistency, I think you have to assume that parameter names could 
be anything.  "outseq" is a popular parameter name for output files of 
type "seqout", "seqoutall", and "seqoutset", and is actually only used 
about 20 times in EMBOSS.

Edgar Crowdy, Programmer                crowdy at
Centre for Computational Biology, Hospital for Sick Children, Toronto

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