[EMBOSS] Seqret stdin issues

[pmr at ebi.ac.uk]

Ronnie wrote:

> Unless anyone has any cocoa-specific/seqret piping
> suggestions? Thanks a lot, fellas!

Just to point out that seqret would also support opening your application
as a pipe from within the USA - should give you the same result. We
support perl-style pipe definitions to launch applications as input files.
This is a feature of EMBOSS from the early days which nobody has (as far
as we know) used very much.

You can also launch applications as database access methods, defining the
application, sending some "id" to the command line for the application,
and reading the results in seqret in some format definied in the database
definition.

One point on reading from stdin ... EMBOSS 3.0.0 should be able to handle
various carriage return/line feed file formats, but earlier releases may
occasionally have problems.

Running seqret with "-debug" on the commandline will create a seqret.dbg
file that should help tell you what is going on - for example, how far it
gets with trying to read your stdin input file. If you;re not sure what
the seqret.dbg file contents mean, you can send the file to me and I'll he
happy to take a look.

Have fun!

Peter