[Pipet Users] Re: [nocat] SEALS

J.W. Bizzaro jeff at bioinformatics.org
Mon May 14 19:39:29 EDT 2001

Roland Walker wrote:
> If there is some format you need to export
> command-line options, I'd be glad to support it.

When CLI programs are piped together, in Piper or elsewhere, they're something
like linked libraries: whoever or whatever does the linking needs to know
something about the I/O parameters.  The problem is, CLI programs don't
provide that information prior to execution.  They *DO* however have
human-readable help output (by typing the --help or -h flag).  In Piper,
programs can be wrapped/ported by hand.  But we'd like to automate the
process, and probably the best way to do this would be to parse the help
output.  There seems to be some semblence of a standard, when you look at the
output, but I don't believe that there is any.  Anyway, if we find the least
common denominator, we may try promoting it for CLI programs.

Unless someone can think of a better way.  We've also considered parsing man
files and source code.

J.W. Bizzaro                                jeff at bioinformatics.org
Director, Bioinformatics.org        http://bioinformatics.org/~jeff
"As we enjoy great advantages from the inventions of others, we
should be glad of an opportunity to serve others by any invention
of ours; and this we should do freely and generously."
                   -- Benjamin Franklin

More information about the Pipet-Users mailing list