needle -filter

[Peter Rice]

simon andrews (BI) wrote:

> One quick extra feature request though.  For the asis:: USA, would it be
> possible to assign a name to the sequences passed in, even if it's 
> only 1,2,3 or seq1 seq2 seq3 etc.  It would make parsing of output files
> much easier.  A way to specify a name in the USA would be even better
> (eg asis::name>GAGAGTGTAGT or whatever).

Should be possible to do this:

needle asis::aaacccgggttt -sid simon asis::aacccgg -sid peter -filter

but there is a problem with the second -sid for needle because it is a 
seqall input, and specifying the id is a problem with possibly more than 
one input.

We can look into allowing -sid for seqall input, for the first sequence 
in the stream.

Peter