[EMBOSS] changing the default output file name

[Rozenbaum, Daniel (Biocceleration Inc)]

Greetings,

We're trying to figure out how to change the default output file naming mechanism of some of the EMBOSS tools.

As http://emboss.sourceforge.net/developers/acd/syntax.html explains: "The output filename is constructed from the name: and extension: attributes in a $( name).$(extension) format. If the name: attribute is not defined in the ACD file, it will default to the calculated attribute name: of the FIRST sequence that is read in ($(asequence.name) if the sequence parameter is named asequence). The extension: attribute will default to the program name, and is usually left as the default value."

Taking fuzzpro as an example, the default name of the output file for "fuzzpro -sequence tsw -pattern <pattern>" is "12s1_arath.fuzzpro".

What we'd like to achieve is for the base of the output file name to consist of the value of the -sequence parameter. So in the example above the default output file name would be "tsw.fuzzpro".

Our first attempt to achieve this consisted of adding ' rname: "$(sequence)" ' in ' section: output' of fuzzpro.acd . This appears to work fine when the value of -sequence is a database name like in the example above, but breaks if the value of -sequence is, for example, a path to a list file.

We were hoping to find an existing way to apply a regex substitution to the value of $(sequence) in the ACD file, but it appears that no such mechanism exists at this time.

Any and all advice would be greatly appreciated!

Many thanks,
Daniel

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Daniel Rozenbaum
Biocceleration, Inc.
OCIO/Office of Application Engineering & Development/Patent System Division
600 Dulany St.
Alexandria, VA 22314