Path: utzoo!utgpu!jarvis.csri.toronto.edu!mailrus!umich!samsung!brutus.cs.uiuc.edu!psuvax1!psuvm!MSHRI!CLARK
From: clark@MSHRI.UTORONTO.CA
Newsgroups: bit.listserv.info-gcg
Subject: RE:      User Interface
Message-ID: <9002100341.AA04022@lash.utcs.utoronto.ca>
Date: 10 Feb 90 03:41:23 GMT
Sender: "INFO-GCG: GCG Genetics Software Discussion" <INFO-GCG@UTORONTO>
Reply-To: clark@MSHRI.UTORONTO.CA
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   Ellis Golub (GOLUB @ PENNDRLS (Bitnet)) writes:

/Question: Does anybody know enough DCL (or have a better solution)
/to doing automated multiple file conversions with (for example) FROMIG.
/I hit upon the idea of putting all the sequences in one file, but
/this solution, while effective, is not general or elegant. I would
/appreciate hearing from anyone with an idea or a solution.

   I would have replied sooner, but I've been a bit behind with my work and
sleep recently, what with all the activity on info-gcg. Since it's for a
good cause, I don't mind too much.

   Here's a small command procedure that will probably do what you want. It's
not very flexible in that it will only work with FROMIG, but you can use it
as a base to hack up and add the features you want. The procedure was made a
bit more difficult than I expected because (don't laugh) FROMIG doesn't take
command line arguments. BTW (By The Way), this is a theoretical program in
that I haven't actually tested it to make sure it will work, but it is
conceptually sound even if there may be some little syntactical errors in it.

$ ! Convert IG format files to GCG format.
$ ! Specify the files to convert on the command line, using regular DCL
$ ! filename wildcards if desired. If no name is specified on the command
$ ! line, convert all files (in the current directory) with
$ ! the specification *.IG.
$
$ if("''p1'" .EQS. "") then p1 := "*.IG"        ! If no command line name
$ open/write comfile IGCONVERT.CMD              ! Make a temp command procedure
$
$loop_start:
$
$       file = f$search(p1)
$       if(file .EQS. "") then goto outa_loop
$       write comfile "$ FROMIG"                ! Start the program
$       write comfile "''file'"         ! Give it the file to convert
$
$goto loop_start
$
$outa_loop:
$
$ close comfile                         ! Close the temporary command procedure
$ @IGCONVERT.CMD                        ! Execute it
$ delete IGCONVERT.CMD;*                ! Clean up the droppings


   Hope this is the kind of thing you were looking for.


Stephen Clark

clark@mshri.utoronto.ca  (Internet)
sinai@utoroci            (Netnorth/Bitnet)

"We should be quite remiss not to emphasize that despite the popularity of
secondary structural prediction schemes, and the almost ritual performance
of these calculations, the information available from this is of limited
reliability. This is true even of the best methods now known, and much more
so of the less successful methods commonly available in sequence analysis
packages. Running a secondary structure prediction on a newly-determined
sequence just because everyone else does so, is to be deplored, and the
fact that the results of such predictions are generally ignored is
insufficient justification for doing and publishing them."
   - Arthur Lesk, 1988