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chopuping multiple files

Karl Smalley K_Smalley at lac.jci.tju.edu
Fri Jan 9 17:31:11 EST 1998


Harry Hahn wrote:

> I recently had to run chopup on a large number of
> automated-sequencer-generated sequences and discovered "chopup *" does
> not
> work. Then I had to reverse the sequences and discovered "reverse" has
> the
> same, um, "feature."
>
> Any suggestions on how to make this process easier? We're running the
> Korn
> shell and I imagine there's a way but I'm stumped for now and would
> appreciate some pointers.
>
> Thanks,
> Harry
>
> --
> Harry Hahn <h3 at ucla.edu>
> Research and Instructional Biocomputing Services - UCLA


The following script was written in csh.  Sorry, don't have access to
the korn shell (nor do I know much about it).  If you have the csh
installed in /bin then this script should work (you'll probably have to
insert the csh specific gcgstartup scripts also).  Or (probably better),
you might be able to translate the csh script to a ksh script.

------------------- 8< ----- Begin Snip Here --------->8 ---------
#!/bin/csh
#
#  multi_gcg_csh
#
#  created by Karl J. Smalley on 1/9/98
#
#  usage:
#
#     multi_gcg_csh "gcg command with paramaters" *.seq
#
#     The double-quotes are only neccesary for commands that are
multiple
#     words or require command line options.  For example the following
#     works fine:
#
#     multi_gcg_csh reformat *.seq
#
# purpose:
#
#     The purpose of this csh script is to facilitate running the same
#     gcg command on mutiple files.  Since the script just reruns the
#     program many times with each file in the argument list, the user
#     will be prompted for any input on each and every file.  For
example
#
#     multi_gcg_csh chopup *.txt
#
#     will ask for the output file name for every file with the
extension
#     .txt (each time chopup is run).  However,
#
#     multi_gcg_csh "chopup -DEF"  *.txt
#
#     will run accepting all defaults, which for chopup would replace
.txt
#     with .dat on the copped up output file, with out stopping for user

#     input.
#
##############################################################################

echo $0 " now processing " $argv
if ($#argv < 2) goto usage

# :q appended so that multiple word argument is treated as one string

if ($argv[1]:q == "-h") goto usage
if ($argv[1]:q == "-?") goto usage
if ($argv[1]:q == "-help") goto usage
if ($argv[1]:q == "help") goto usage
@ i = 2
while($i <= $#argv)
        echo $1 $argv[$i]
        $1 $argv[$i]
        @ i++
end
exit
usage:
        more $0

------------------- 8< ----- End Snip Here --------->8 ---------

Hope this is of some help to you.

--
----------------------------------------------------------------------
Karl J. Smalley
Systems Analyst
                                          Snail Mail:
Phone:  (215) 503-4602                      Kimmel Cancer Center
FAX:    (215) 923-2117                      Thomas Jefferson University
E-Mail: mailto:K_Smalley at lac.jci.tju.edu    812 BLSB, 233 S. 10th St.
WWW     http://www.jci.tju.edu/~karl        Philadelphia, PA 19107

"Mate in 3" - The sweetest words I have ever heard myself utter.
*******  This is  a Chess Phrase and nothing more **********
------------------------------------------------------------------------


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