Bash to select text and apply it to a selected file in bash
In the bash below I am asking the user for a panel and reading that into bed. Then asking the user for a file and reading that into file1.Is the grep in bold the correct way to apply the selected panel to the file? I am getting a syntax error. Thank you
Code:
FILESDIR=/home/cmccabe/Desktop/ref/validation/val
PANELDIR=/home/cmccabe/Desktop/ref/validation/panels
PS3="please select a panel: "
cd "$PANELDIR"
select bed in $(ls *.txt)
do [ "$panel" != "" ] && break
done
PS3="please select a file to analyze with a panel: "
cd "$FILESDIR"
select file1 in $(ls *.vcf)
do [ "$file1" != "" ] && break
done
printf "FILE is: ${file1} and will be used filtered to ${panel} \n"
read -r -p "Is this correct? [y/N] " response
if [[ $response =~ ^[nN][oO]?$ ]]
then
echo 'please try again' && exit
else
logfile="/home/cmccabe/Desktop/ref/validation/val/process.log"
for f in /home/cmccabe/Desktop/ref/validation/val/$file1 ; do
echo "Start filter creation: $(date) - File: $f"
bname=$(basename $f)
pref=${bname%%_*.vcf}
grep -wFf /home/cmccabe/Desktop/ref/validation/panels/$panel $f >/home/cmccabe/Desktop/ref/validation/filtered/${pref}_filtered.txt
echo "End filder creation: $(date) - File: $f"
done >> "$logfile"
line 32: syntax error: unexpected end of file
Last edited by cmccabe; 09-29-2016 at 05:48 PM..
Reason: fixed typo
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LEARN ABOUT OPENSOLARIS
panel_hidden
panel_show(3CURSES) Curses Library Functions panel_show(3CURSES)NAME
panel_show, show_panel, hide_panel, panel_hidden - panels deck manipulation routines
SYNOPSIS
cc [ flag ... ] file ... -lpanel-lcurses [ library .. ]
#include <panel.h>
int show_panel(PANEL *panel);
int hide_panel(PANEL *panel);
int panel_hidden(PANEL *panel);
DESCRIPTION
show_panel() makes panel, previously hidden, visible and places it on top of the deck of panels.
hide_panel() removes panel from the panel deck and, thus, hides it from view. The internal data structure of the panel is retained.
panel_hidden() returns TRUE(1) or FALSE(0) indicating whether or not panel is in the deck of panels.
RETURN VALUES
show_panel() and hide_panel() return the integer OK upon successful completion or ERR upon error.
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|MT-Level |Unsafe |
+-----------------------------+-----------------------------+
SEE ALSO curses(3CURSES), panel_update(3CURSES), panels(3CURSES), attributes(5)NOTES
The header <panel.h> automatically includes the header <curses.h>.
SunOS 5.11 31 Dec 1996 panel_show(3CURSES)
09-29-2016
