[EMBOSS] Antwort: Genbank GI fetching?

[Niels Larsen]

david.bauer at bayerhealthcare.com wrote:
> Hi Niels,
> 
> Niels Larsen <niels at genomics.dk> schrieb am 18/06/2007 01:56:40:
> 
>> Btw, the seqret documentation
>> doesnt say, but stdin: works as stdout:
>>
>> zcat 2.gz | seqret -filter stdin:AAIY01677200 -sbegin1 11 -osformat2
>> embl -firstonly
> 
> Ehm, this is a strange construction. The -filter is a general qualifier 
> for all EMBOSS programs and means that input comes from stdin and output 
> goes to stdout. So I'm not sure what happens if you combine -filter with 
> stdin: but I guess that Peter has an answer to this.

It was my first way to get only a particular entry from the stream,
but there could well be a better way .. next I will be looking for
a way to get several out of the stream, instead of one, with pure
command line .. could use a list file, but then my code that makes
these command lines would need to manage those on the fly ..

I found a little trap with seqret, if one enters by mistake --firstonly
(the GNU way) instead of -firstonly, then seqret quietly returns
nothing. It should probably complain instead, the other arguments
do that. I use 4.1.0.

Niels L