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Full Discussion: Naming output files based on variable parameters and input filenames
Top Forums Shell Programming and Scripting Naming output files based on variable parameters and input filenames Post 302931338 by sea on Monday 12th of January 2015 02:21:58 PM
Old 01-12-2015
output=$file is empty.
That is because it is outside the loop, try to place it 2 lines lower.
Therefor both, the current and your 'future' line:
Code:
 do process --out=$output."tab" <options> $file ;

Looks in plaintext:
Code:
 do process --out=."tab" <options> Value_from_Find ;

Or at best (with the thought change):
Code:
 do process --out=Value_from_Find."tab" <options> Value_from_Find ;

For the moment, try:
Code:
#!/usr/bin/bash
model=1
for file in $(find /path/to/files/AG00*/*/ -type f -name 'AG00*.fa');
 do output=$file
      process --out=$output."tab" <options> $file ;
      echo $file
done

Hope this helps

EDIT:
model=1 is not used and could be deleted.
 

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LEARN ABOUT XFREE86

dh_compress

DH_COMPRESS(1)							     Debhelper							    DH_COMPRESS(1)

NAME
       dh_compress - compress files and fix symlinks in package build directories

SYNOPSIS
       dh_compress [debhelperoptions] [-Xitem] [-A] [file...]

DESCRIPTION
       dh_compress is a debhelper program that is responsible for compressing the files in package build directories, and makes sure that any
       symlinks that pointed to the files before they were compressed are updated to point to the new files.

       By default, dh_compress compresses files that Debian policy mandates should be compressed, namely all files in usr/share/info,
       usr/share/man, files in usr/share/doc that are larger than 4k in size, (except the copyright file, .html and other web files, image files,
       and files that appear to be already compressed based on their extensions), and all changelog files. Plus PCF fonts underneath
       usr/share/fonts/X11/

FILES
       debian/package.compress
	   These files are deprecated.

	   If this file exists, the default files are not compressed. Instead, the file is ran as a shell script, and all filenames that the shell
	   script outputs will be compressed. The shell script will be run from inside the package build directory. Note though that using -X is a
	   much better idea in general; you should only use a debian/package.compress file if you really need to.

OPTIONS
       -Xitem, --exclude=item
	   Exclude files that contain item anywhere in their filename from being compressed. For example, -X.tiff will exclude TIFF files from
	   compression.  You may use this option multiple times to build up a list of things to exclude.

       -A, --all
	   Compress all files specified by command line parameters in ALL packages acted on.

       file ...
	   Add these files to the list of files to compress.

CONFORMS TO
       Debian policy, version 3.0

SEE ALSO
       debhelper(7)

       This program is a part of debhelper.

AUTHOR
       Joey Hess <joeyh@debian.org>

11.1.6ubuntu2							    2018-05-10							    DH_COMPRESS(1)
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