[emboss-dev] Specifying sequence lists for seqret

Peter Rice pmr at ebi.ac.uk
Thu Jul 29 12:28:33 UTC 2010

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)?


Peter Rice

More information about the emboss-dev mailing list