[emboss-dev] Specifying sequence lists for seqret

[Peter Rice]

On 29/07/10 12:47, Rimvydas Naktinis wrote:
> Hi,
>
> I'm developing EMBOSS integration into Chipster project
> (chipster.csc.fi). I was wondering if there's a way to specify sequence
> list (for example, when calling seqret) without creating any extra files?
>
> I know there's a way to do it like this:
>>  seqret @sequencelist
> or
>>  seqret list:sequencelist
>
> But what I would need would look something like:
>>  seqret "swiss:CASA1_RABIT,swiss:CASA1_HUMAN"
>
> I've looked into USA format specification and it seems that there is
> actually no way to do it without creating some temporary file. Or am I
> missing something?

We can add that as an option ... but there is a very real danger that 
the command line will be too long.

How many sequences will be on the command line (normal use, and worst case)?

regards,

Peter Rice