Naming output files based on variable parameters and input filenames
Hello, I have a series of files in sub-directories that I want to loop through, process and name according to the input filename and the various parameters I'm using to process the files. I have a number of each, for example file names like AG005574, AG004788, AG003854 and parameter values like ATd, PZa, RTK1, so I want to end with files like AG005574_ATd, AG005574_PZa, AG005574_RTK1, AG004788_ATd, etc.
I loop through the subfolders, run the process and output the results like so:
Code:
#!/usr/bin/bash
model=1
output=$file
for file in $(find /path/to/files/AG00*/*/ -type f -name 'AG00*.fa');
do process --out=$output."tab" <options> $file ;
echo $file
done
Obviously, this names the file by process only, not by process_input, and it only writes one file (the last processed) because it over-writes the others. In the case above, the --out= seems to me to be the key to change to get what I want, but $output$file and variations don't work.
I'm sure this is not a tricky problem but I haven't been able to find or piece together a solution. Any help/tutoring is much appreciated.
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Last edited by Scrutinizer; 01-12-2015 at 02:40 PM..
Reason: repaired code tags
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LEARN ABOUT FREEBSD
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)
01-12-2015
