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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LEARN ABOUT SUNOS
gnome-desktop-item-edit
gnome-desktop-item-edit(1) User Commands gnome-desktop-item-edit(1)NAME
gnome-desktop-item-edit - GNOME Desktop file editor
SYNOPSIS
gnome-desktop-item-edit [--create-new] filename
DESCRIPTION
gnome-desktop-item-edit is the GNOME Desktop file editor, which you can use to create or edit the .desktop (known as desktop) file. GNOME
uses a standard desktop file specification as proposed by freedesktop.org. A desktop file consists of a number of name-value pairs that
define how a desktop should organize a particular application. As this is defined as an open standard, integration of applications into
GNOME Desktop is relatively straightforward.
A basic entry in the desktop file must start with a tag called [Desktop Entry]. It can then have a number of name-value pairs as defined by
the standard. The minimum entries are as follows:
Name the name of the application
Comment a textual description of the application which is displayed as a tooltip message by gnome-panel. When set appropri-
ately, the comment can be localized within the same file.
Exec the name of the actual executable
Icon the file name of the icon image
Type the desktop file type
Categories a multi-string field which is used by gnome-panel to group applications into the appropriate categories.
These desktop files provide the information to gnome-panel, which places the application in the appropriate locations on the panel. In
a similar manner, the GNOME file manager (Nautilus) uses information from the desktop files to display the 'applications:///' view.
OPTIONS
The following options are supported:
--create-new Creates a new .desktop file.
OPERANDS
The following operands are supported:
filename The name of the desktop file to be edited or viewed.
EXAMPLES
Example 1: Editing an existing .desktop file
example% gnome-desktop-item-edit fullpath/filename
This command invokes the launcher dialog and loads the contents of the specified desktop file into the relevant fields.
EXIT STATUS
The following exit values are returned:
0 Application exited successfully
>0 Application exited with failure
FILES
The following files are used by this application:
/usr/bin/gnome-desktop-iExecutable for GNOME Desktop file editor
/usr/share/applications/Desktopofile
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWgnome-panel |
+-----------------------------+-----------------------------+
|Interface stability |External |
+-----------------------------+-----------------------------+
SEE ALSO gnome-panel(1), nautilus(1)
Latest version of the GNOME Desktop User Guide for your platform.
NOTES
Written by Ghee Teo, Sun Microsystems Inc., 2003.
SunOS 5.10 2 Oct 2003 gnome-desktop-item-edit(1)
02-07-2017
.