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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