Undefined "n" value and simplifying script Post: 302496123

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Top Forums Shell Programming and Scripting Undefined "n" value and simplifying script Post 302496123 by Xterra on Saturday 12th of February 2011 10:35:05 AM

02-12-2011

Registered User

Calculating matrix distances and generating a tree

Franklin52,
Let me try to explain what I am trying to accomplish. I have hundreds of files named "block1", "block2", etc; containing DNA sequences in Phylip format. I want to calculate the genetic distance for each "block" file using the binary program "dnadist" which uses D (Kimura) and Y (YES) as options. Unfortunately, "dnadist" won't let me use anything as an input but a file named "infile". Thus, I start my script by renaming the files from "blockX" to infile and then feed it into dnadist. The output file that is generated by "dnadist" is bydefault "outfile" and I cannot change the file name either. I just came to realize that I do not need to "temporarily" rename the "outfile" to "ResultX" but instead to "infile", therefore I can delete that part. Finally, I grab the "new" "infile" and process it using "neighbor", using Y (YES) as option, in order to generate the corresponding trees. "neighbor" generates two different files "outfile" and "outtree", I only need the "outtree" file, which I rename as "ResultX", and that' why I just need to delete the "outfile". Then, we process the next file "block2" and the cycle starts again.
As I said, many times I do not know the number of "block" files in my folder, and therefore I would like to modify my script to be able to process whatever number of files, it can range from some few to several hundreds, are present in that given folder.
So, the my script now looks something like this:

Code:

#!/bin/bash
for i in {1..2}
do
 mv block${i} infile
 ./dnadist <<-EOF
 D
 Y
 EOF
 rm infile
 mv outfile infile
 ./neighbor <<-EOF
 Y
 EOF
 rm infile
 rm outfile
 mv outtree Result${i}
done

Thanks!

Last edited by Xterra; 02-12-2011 at 11:41 AM..

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shcomp

SHCOMP(1)						       Korn shell utilities							 SHCOMP(1)

NAME

       shcomp - compile a shell script

SYNOPSIS

       shcomp [ options ] [infile [outfile]]

DESCRIPTION

       Unless  -D is specified, shcomp takes a shell script, infile, and creates a binary format file, outfile, that ksh can read and execute with
       the same effect as the original script.

       Since aliases are processed as the script is read, alias definitions whose value requires variable expansion will not work correctly.

       If -D is specified, all double quoted strings that are preceded by $ are output. These are the messages	that  need  to	be  translated	to
       locale specific versions for internationalization.

       If  outfile  is omitted, then the results will be written to standard output. If infile is also omitted, the shell script will be read from
       standard input.

OPTIONS

       [D dictionary] Generate a list of strings that need to be placed in a message catalog for internationalization.	[n noexec] Displays  warn-
       ing messages for obsolete or non-conforming constructs.	[v verbose] Displays input from infile onto standard error as it reads it.

EXIT STATUS

       0
	 Successful completion.
       >0
	 An error occurred.

SEE ALSO

       ksh(1)

IMPLEMENTATION

     version
       shcomp (AT&T Research) 2003-03-02
     author
       David Korn <dgk@research.att.com>
     copyright
       Copyright (c) 1982-2010 AT&T Intellectual Property
     license
       http://www.opensource.org/licenses/cpl1.0.txt

								    2003-03-02								 SHCOMP(1)

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