[EMAIL PROTECTED] wrote: > Hi Niels, > > Niels Larsen <[EMAIL PROTECTED]> 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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
