[EMBOSS] transeq feature/bug

[Peter Rice]

Marc Logghe wrote:
> Hi all,
> 
> A Pise user reported the following issue when running transeq: the
> resulting translation is dependant on the order of the input sequences.
> 
> As it seems, transeq takes the length of the first sequence and uses
> that range to translate. Which is fine, but that range is used as well
> for all the sequences that are coming after, which is wrong.
> 
> If it happens that your first sequence in the list is smaller than the
> ones coming after, then all translations are truncated.
> 
> I think that is a bug.

Strange - we have QA tests for exactly those cases and they are working
in releases 5.0.0 and earlier releases.

Ah, but perhaps this is a Pise problem. If Pise is putting -send on the
command line with the length of the first sequence, then this will make
EMBOSS apply the same end position to all sequences.

Can you please check the command line Pise is using and if that is not
the cause then send the command line and example inputs.

regards,

Peter Rice