Using method: app for seq retrieval

[Peter Rice]

Gene Cutler wrote:
> In my emboss config, I've put
> this:
> 
> DB test [
>          method: app
>          format: fasta
>          app: "/usr/local/bin/test.pl %s"
>          type: N
> ]
> 
> and then typed:
> seqret test:XYZ
> 
> but I get:
> Error: Unable to read sequence 'test:XYZ'
> 
> If I run "/usr/local/bin/test.pl XYZ" from the command line, it prints
> out
> the fasta sequence properly.

The definition looks right to me. As a check, can seqret read the fasta
file that it writes (in case it has bad characters).

Seqret will check the sequence ID from the fasta format is 'XYZ'. It does
this because you are passing this as a database USA (test:XYZ) so it acts
like a database search and tests the 'id'. I think this is the most likely
cause.

You can add a few "print STDERR" lines to your perl script to check it is
being executed, and what happens.

You can also try seqret with -debug on the command line to get a seqret.dbg
file that should help trace the problem.

>I also tried this:
>DB test [
>         methodsingle: app
>         format: fasta
>         app: "/usr/local/bin/test.pl %s"
>         type: N
>]
>
>but that's even worse:
>Error: Bad database attribute 'methodsingle'

methodentry, not methodsingle.

Was this an error in the documentation somewhere, or just a bad guess?

regards,

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723