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a q s

EXTERNAL uses an external application to retrieve sequences. The ID is passed as an argument to the application, either replacing %s in the command string (if present) or as an additional argument (if there is no %s).

EXTERNAL requires the application to return the sequence on STDOUT. If the application writes to somewhere else, simply wrap it in a script that copies the output to STDOUT.

DB mydb [
#required parameters
    method: "app"
    format: "fasta"
    type: "P"
    app: "getfromdb"
#optional parameters
    comment: "my own protein database with a custom retrieval program"
    app: "getfromdb mydatabase \%s"

The first app: definition will use the default call 'getfromdb mydb:id'

The alternative app: definition will use the %s format and call 'getfromdb mydatabase id'

Both will pass either the ID or accession from the query, so that USAs mydb-id:x13776 and mydb-acc:x13776 are equivalent.

Peter Rice 2007-04-26