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Full Discussion: loop through numbered filenames
Top Forums Shell Programming and Scripting loop through numbered filenames Post 302313233 by polly_falconer on Tuesday 5th of May 2009 05:31:45 AM
Old 05-05-2009
loop through numbered filenames
Hi I'm very new to this script thing, so please be gentle.

I am trying to get a command - the mach2qtl command in the code below - to loop through a set of files.
Each command should take the same two .dat and .ped files, but the .mlinfo and .mlprob files with filenames including 'chrom1' should be run together and output to a file PC_full_1.txt

I have run the command fine by retyping it using the appropriate file names, but would like to run this as a script that runs through files 1 - 22.

When I run the script below I get a segmentational error.

What am I doing wrong?

Thanks,

Polly

Code:
 
#! /bin/bash
# program to run through each chromosome carrying out association using mach2qtl
 

# increment through chromosome numbers
i=0
while [ $i -lt 23 ]
        do
                i=$(( $i +1 ))
#list info and prob files 1 - 22
                infofile=chrom$i_step2.mlinfo
                probfile=chrom$i_step2.mlprob
# run mach2qtl using the above specified files
                mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile > PC_full_$i.txt

done
exit 0

 

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LEARN ABOUT SUNOS

gst-complete-0.8

gst-complete-0.8(1)						   User Commands					       gst-complete-0.8(1)

NAME

       gst-complete-0.8, gst-complete - perform bash completion for gst-launch command lines

SYNOPSIS

       complete -Cgst-complete-0.8 gst-launch

       gst-complete [--gst-list-mm] [--gst-mm=string] [--print]

DESCRIPTION

       gst-complete-0.8 enables bash to provide context-sensitive tab completion for gst-launch command lines. See gst-launch(1) for the syntax of
       gst-launch command lines.

       You must have a version of bash that supports programmable completion. Such versions of bash provide the complete built-in command.

       gst-complete is a wrapper script that runs the latest installed version of gst-complete-X.X. For example, if both gst-complete-0.7 and gst-
       complete-0.8 are installed on your system, gst-complete runs gst-complete-0.8.

OPTIONS

       The following options are supported by gst-complete-0.8 and gst-complete:

       --help	       Display detailed usage message. You can also use -? to specify this option.

       The following options are supported by gst-complete only:

       --gst-list-mm   List found major/minor versions. This option displays the versions that are available.

       --gst-mm=string Force  major/minor  version.  This  option  enables you to specify a specific version to run, if you do not want to run the
		       default version.

       --print	       Print wrapped command line. This option displays the command that will be run, and then runs the command.

EXAMPLES

       Example 1: Generating the Registry of Available Plugins by Running gst-compprep

       Run the following command in your .bash_profile or other appropriate place:

       example% complete -C gst-complete-0.8 gst-launch

       Example 2: Running the Wrapper Script and Displaying the Command Name

       example% gst-complete --print
       /usr/bin/gst-complete-0.8

FILES

       The following files are used by this application:

       /usr/bin/gst-complete-0.Executable for bash completion for gst-launch

       /usr/bin/gst-complete   Wrapper script that runs the latest installed version of gst-complete-X.X

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWgnome-media		   |
       +-----------------------------+-----------------------------+
       |Interface stability	     |External			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       gst-compprep(1), gst-feedback(1), gst-inspect(1), gst-launch(1), gst-launch-ext(1), gst-md5sum(1), gst-register(1), gst-thumbnail(1),  gst-
       typefind(1), gst-xmlinspect(1), gst-xmllaunch(1), gstreamer-properties(1), libgstreamer-0.8(3), libgstgetbits(3)

NOTES

       Original man page written by the GStreamer team at http://gstreamer.net/.

       Updated by Brian Cameron, Sun Microsystems Inc., 2004.

SunOS 5.10							    14 Oct 2004 					       gst-complete-0.8(1)
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