Bash looking in different directory for file that isn't referenced in command
When I run the below bash I get the expected output, which is the sum of all matching targets less than 20 in $file1. The filename in the directory is fixed (in bold).
Code:
for file1 in /home/cmccabe/Desktop/test/panel/reads/16-0000_EPIL70.txt ; do
bname=`basename $file1`
pref=${bname%%_*.txt}
awk '{gsub(/[()]/,_)} \
count[$5]==""{ count[$5]=0 }
$7 < 20{ count[$5]++}
END{
for(k in count)
printf "%s %d\n", k, count[k]
}' $file1 > /home/cmccabe/Desktop/test/panel/20x/base/16-0000_allepil70.bed
done
The desired bash is the exact same except the unique numerical digits, 16-0000 are read into a variable {pref}. This is because there can be multiple files with the same extension, but the digits are always unique.
Code:
for file1 in /home/cmccabe/Desktop/test/panel/reads/${pref}_EPIL70.txt ; do
bname=`basename $file1`
pref=${bname%%_*.txt}
awk '{gsub(/[()]/,_)} \
count[$5]==""{ count[$5]=0 }
$7 < 20{ count[$5]++}
END{
for(k in count)
printf "%s %d\n", k, count[k]
}' $file1 > /home/cmccabe/Desktop/test/panel/20x/base/${pref}_allepil70.bed
done
awk: fatal: cannot open file `/home/cmccabe/Desktop/test/panel/reads/16-0000_epil70lessthan20xregions.txt_EPIL70.txt' for reading
The file that it is looking for is not in that directory, but not sure why it is even looking for it as I do not reference it at all in the command or do I? Thank you .
Code:
ls -l /home/cmccabe/Desktop/test/panel/reads
total 10952
-rw-rw-r-- 1 cmccabe cmccabe 11214550 Feb 7 07:27 16-0000_EPIL70.txt
Last edited by cmccabe; 02-07-2017 at 11:49 AM..
Reason: fixed format,
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Discussion started by: bodisha
4 Replies
LEARN ABOUT DEBIAN
sysprofile
SYSPROFILE(8) System Manager's Manual SYSPROFILE(8)NAME
sysprofile - modular centralized shell configuration
DESCRIPTION
sysprofile is a generic approach to configure shell settings in a modular and centralized way mostly aimed at avoiding work for lazy sysad-
mins. It has only been tested to work with the bash shell.
It basically consists of the small /etc/sysprofile shell script which invokes other small shell scripts having a .bash suffix which are
contained in the /etc/sysprofile.d/ directory. The system administrator can drop in any script he wants without any naming convention
other than that the scripts need to have a .bash suffix to enable automagic sourcing by /etc/sysprofile.
This mechanism is set up by inserting a small shell routine into /etc/profile for login shells and optionally into /etc/bashrc and/or
/etc/bash.bashrc for non-login shells from where the actual /etc/sysprofile script is invoked:
if [ -f /etc/sysprofile ]; then
. /etc/sysprofile
fi
For using "sysprofile" under X11, one can source it in a similar way from /etc/X11/Xsession or your X display manager's Xsession file to
provide the same shell environment as under the console in X11. See the example files in /usr/share/doc/sysprofile/ for illustration.
For usage of terminal emulators with a non-login bash shell under X11, take care to enable sysprofile via /etc/bash.bashrc. If not set
this way, your terminal emulators won't come up with the environment defined by the scripts in /etc/sysprofile.d/.
Users not wanting /etc/sysprofile to be sourced for their environment can easily disable it's automatic mechanism. It can be disabled by
simply creating an empty file called $HOME/.nosysprofile in the user's home directory using e.g. the touch(1) command.
Any single configuration file in /etc/sysprofile.d/ can be overridden by any user by creating a private $HOME/.sysprofile.d/ directory
which may contain a user's own version of any configuration file to be sourced instead of the system default. It's names have just to
match exactly the system's default /etc/sysprofile.d/ configuration files. Empty versions of these files contained in the $HOME/.syspro-
file.d/ directory automatically disable sourcing of the system wide version.
Naturally, users can add and include their own private script inventions to be automagically executed by /etc/sysprofile at login time.
OPTIONS
There are no options other than those dictated by shell conventions. Anything is defined within the configuration scripts themselves.
SEE ALSO
The README files and configuration examples contained in /etc/sysprofile.d/ and the manual pages bash(1), xdm(1x), xdm.options(5), and
wdm(1x). Recommended further reading is everything related with shell programming.
If you need a similar mechanism for executing code at logout time check out the related package syslogout(8) which is a very close compan-
ion to sysprofile.
BUGS
sysprofile in its current form is mainly restricted to bash(1) syntax. In fact it is actually a rather embarrassing quick and dirty hack
than anything else - but it works. It serves the practical need to enable a centralized bash configuration until something better
becomes available. Your constructive criticism in making this into something better" is very welcome. Before i forget to mention it: we
take patches... ;-)
AUTHOR
sysprofile was developed by Paul Seelig <pseelig@debian.org> specifically for the Debian GNU/Linux system. Feel free to port it to and use
it anywhere else under the conditions of either the GNU public license or the BSD license or both. Better yet, please help to make it into
something more worthwhile than it currently is.
SYSPROFILE(8)
02-07-2017
.