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Combining chopup and reformat?

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Tue Oct 24 06:26:55 EST 1995

In <DGxDo0.Lu9 at argo.net> mcoyne at argo.net writes:

> Can anyone tell me of a way to combine chopup and reformat commands in
> GCG?  What I'm looking for is perhaps a way to define a command that
> would take as an argument a filename, run this through chopup, and
> pass the output to reformat, resulting in a GCG format file.
> We get our files in flat ASCII format with no carriage
> return/linefeeds.  Before they can be Reformatted, therefore, they
> must be passed through Chopup.  I understand how to pass the output
> from chopup to reformat (include /OUT="|reformat /D" on the chopup
> command line), but what I'm looking for is the equivelant of the
> replacable parameter in DOS batch files (eg %1).  Thus I could define
> a command (say "chopgcg") such that one could enter the command:
> $chopgcg sequence1.seq
> and have it run something like:
> chopup %1 /OUT="|reformat /OUT=%1"
> where the %1 would be replaced by the filename indicated as an
> argument on the chopgcg command line, resulting at the end in a file
> called sequence1.seq in proper GCG format.
> Is there a way to do this in OpenVMS?  I'm using version 8.0 of GCG if
> that's helpful.

VMS has no pipes like UNIX. So what you need is a command file like the

   $ chopup 'P1' sys$scratch:interim.file
   $ reformat sys$scratch:interim.file 'P1'
   $ DELETE/NOLOG/NOCONFIRM sys$scratch:interim.file;*

Call this file CHOPGCG.COM and run it with
    @CHOPGCG sequence1.seq

   Christoph Gartmann

| Max-Planck-Institut fuer      Phone   : +49-761-5108-465   Fax: -221       |
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