IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Combining chopup and reformat?

Michael Coyne mcoyne at argo.net
Mon Oct 23 21:48:53 EST 1995


Hello.

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.

Thanks for any suggestions.....

Mike Coyne
mjcoyne at warren.med.harvard.edu





More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net