Using method: app for seq retrieval

Gene Cutler cutler at tularik.com
Mon Jan 21 19:16:17 UTC 2002


I'm trying to follow the docs for using a custom app for sequence 
retrieval.
I made a test perl script which just prints out a fasta sequence to 
stdout,
but I can't get the retrieval to work.  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.

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'

Reads and writes (returns) sequences
Error: No access method for database 'test'
Error: no access method available for 'test:XYZ'
Error: Unable to read sequence 'test:XYZ'


I am using EMBOSS version 2.2.0




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