[EMBOSS] Seqret stdin issues

[Ronnie O]

Just to clarify too about the output of diff, I had it output only the
lines that were different.  So all the other lines of the dbg files
were identical.  I didnt include that in the previous post.
......
Ronnie

On 9/19/05, pmr at ebi.ac.uk <pmr at ebi.ac.uk> wrote:
> 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
>
>