needle -filter

[Jan T. Kim]

On Tue, Jun 10, 2003 at 09:48:04AM +0100, Peter Rice wrote:

> > What Simon needs, and what Emboss doesn't have, is a built in
> > splitter for multisequence files that will allow the individual
> > sequences to be directed to specific inputs in a program like
> > needle.
> 
> You mean needle seq1.txt:abc seq2.txt:xyz
> 
> That is already available!!!!

In the case discussed here it seems that both sequence entries would come
from the same file (e.g. seq1.txt), which is no problem as long as it's
really a file. But what if the file really is an input stream? In that
case, you'd need something like

    needle <stdin>:abc <stdin>:xyz

Technically, this would entail some problems, as entry "xyz" may precede
"abc" in the stream. The needle program would therefore have to scan the
input stream using a list of entries which it needs, scanning twice, as
I'd expect it to happen in

    needle <file>:abc <file>:xyz

will not work with input streams. Perhaps, such capability could be
implemented by defining some special name for the "standard input file"
or "standard input database"? I haven't found such a thing in the USA
specification, but perhaps, that's already invented?

Kind regards, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: kim at inb.uni-luebeck.de                          |
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 *-----=<  hierarchical systems are for files, not for humans  >=-----*