I am trying to create a user prompt while reading a file a line by line in Bash. The idea is for me to plot various files one-by-one using Gnuplot. Here is what I have:
#!/bin/bash
echo "Enter filename that contains the filenames:"
read fname
xr="[1e8:1e20]"
yr="[1:1e13]"
while read line
do
echo -e "reset\nset log\nset xrange$xr\nset yrange$yr\nset xlabel \"Frequency [Hz]\"\nset ylabel \"F_{/Symbol n} [Jy Hz]\"\nset key top left\nplot \"$line.dat\" u 3:(\$3*\$4)*1e26 w l ti \"$line^o\" \n"> plt.gp
gnuplot plt.gp
done < $fname
I would like to enter a user input/"continue?" type thing before "gnuplot plt.gp" command, because at the moment it just plots everything rapidly and then exits. The standard read -p command does not work here. I read somewhere I may need to use file descriptor exec 5 command, but I don't understand. Thanks.
#!/bin/bash
read -p 'Enter filename that contains the filenames: ' fname
xr="[1e8:1e20]"
yr="[1:1e13]"
while read line
do
echo -e "reset\nset log\nset xrange$xr\nset yrange$yr\nset xlabel \"Frequency [Hz]\"\nset ylabel \"F_{/Symbol n} [Jy Hz]\"\nset key top left\nplot \"$line.dat\" u 3:(\$3*\$4)*1e26 w l ti \"$line^o\" \n"> plt.gp
gnuplot plt.gp
read -p 'Do you want to continue? [Y/n]: ' want_to_continue </dev/tty
case "${want_to_continue}" in
Y|y)
continue
;;
*)
echo "OK. Bye!"
break
;;
esac
done < ${fname}
Related
I am new to writing scripts in Bash and I am working on an assignment to make an inventory system. I have written all the scripts and they all work from using the standard input terminal. I now am looking to take the inputs from a text file called a1Input.txt which has all inputs on a new line.
r
9823
r
5430
c
7777
sml_widget
Small Widget (1 oz.)
6.99
15
50
Small, white, widget w/o packaging
r
7777
d
9823
r
9823
r
3293
u
3293
29.99
33
75
r
3293
The code for my initial bash script is this
#!/bin/bash
# assign1.bash
shopt -s nocasematch
option=""
until [ "$option" = "F" ]; do
echo "C - create a new item"
echo "R - read an existing item"
echo "U - update an existing item"
echo "D - delete an existing item"
echo "T - total price of an item"
echo "Choose a option"
read option
case $option in
C)
./create.bash
;;R)
./read.bash
;;U)
./update.bash
;;D)
./delete.bash
;;T)
./total.bash
;;*)
echo "Invalid input"
esac
done
What i would do to inject inputs from file to an interactive script is just:
cat a1Input.txt | ./interactive_script.sh
For example, imagine this simple script (copy-paste on terminal to create):
cat << EOF > questions.sh
#!/bin/bash
echo "What's your name ?"
read name
echo "What is your favourite movie ?"
read movie
echo "Hi \$name, i also love '\$movie' movie !!"
EOF
And these inputs:
cat << EOF > inputs.txt
Edu
Interstellar
EOF
Then, just execute:
chmod a+x questions.sh
cat inputs.txt | ./questions.sh
If your script is more complicated, consider using "expect", although this is quite complex.
BRs
Can anyone help me to modify my script. Because it does not work. Here are three scripts.
1) pb.sh, use delphicpp_release software to read the 1brs.ab.sh and will give the output as 1brs.ab.out
2) 1brs.ab.sh, use for input parameter where a.sh(another script for protein structure), chramm.siz, charmm.crg are file for atom size and charge etc. rest of the parameters for run the delphicpp_release software.
3) a.sh, use for read several protein structures, which will be in the same directory.
my script_1 = pb.sh:
./delphicpp_release 1brs.ab.sh >1brs.ab.out
echo PB-Energy-AB = $(grep -oP '(?<=Energy> Corrected:).*' 1brs.ab.out) >>PB-energy.dat
cat PB-energy.dat
script_2 = 1brs.ab.sh:
in(pdb,file="a.sh")
in(siz,file="charmm.siz")
in(crg,file="charmm.crg")
perfil=70
scale=2.0
indi=4
exdi=80.0
prbrad=1.4
salt=0.15
bndcon=2
maxc=0.0001
linit=800
energy(s)
script_3 = a.sh:
for i in $(seq 90000 20 90040); do
$i.pdb
done
As we don't know what software is, something like
for ((i=90000;i<=100000;i+=20)); do
./software << " DATA_END" > 1brs.$i.a.out
scale=2.0
in(pdb,file="../$i.ab.pdb")
in(siz,file="charmm.siz")
in(crg,file="charmm.crg")
indi=z
exdi=x
prbrad=y
DATA_END
echo Energy-A = $(grep -oP '(?<=Energy>:).*' 1brs.$i.a.out) >>PB-energy.dat
done
A more POSIX shell compliant version
i=90000
while ((i<=100000)); do
...
((i+=20));
done
EDIT: Without heredoc
{
echo 'scale=2.0'
echo 'in(pdb,file="../'"$i"'.ab.pdb")'
echo 'in(siz,file="charmm.siz")'
echo 'in(crg,file="charmm.crg")'
echo 'indi=z'
echo 'exdi=x'
echo 'prbrad=y'
} > $i.ab.sh
./software <$i.ab.sh >$i.ab.out
but as question was changed I'm not sure to understand it.
I have 10 .txt files that contain my data as in output1.txt, output2.txt, output3.txt and so on. I plot this data with the following commands:
#!/bin/bash
gnuplot
set o "output1.png"
p "output1.txt" u 1:2 with lines
set o "output2.png"
p "output2.txt" u 1:2 with lines
set o "output3.png"
p "output3.txt" u 1:2 with lines
and so on.
Obviously when I have like 100 data files, this approach is not very useful. How can I write a shell script that basically automates saving my data into files with a for loop in a script? Is it even possible or should I turn somewhere else like a python script?
I guess you require something like this:
for each in output*.txt
do
BASE_NAME=$(basename $each .txt)
echo ${BASE_NAME}
gnuplot <<- EOF
set o "${BASE_NAME}.png"
p "$each" u 1:2 with lines
EOF
done
Completely untested:
#!/bin/bash
for fn in $(ls output*.txt); do
# Extract file "ID"
fid=${fn:6:(-4)}
# Build output png
out=output${fid}.png
# Echo the commands
echo set o "${out}"
echo p "${fn}" u 1:2 with lines
done
Which you'd either pipe directly into gnuplot:
./abovescript.sh | gnuplot
Or redirect into a script file, then call using gnuplot
./abovescript.sh > myscript
gnuplot myscript
Updated per Mark Setchell's suggestions:
for fn in output*.txt; do
# Extract the file "base"
fid=${fn%%.txt}
# Build output png
out=${fid}.png
# Echo the commands
echo set o \"${out}\"
echo p \"${fn}\" u 1:2 with lines
done | gnuplot
This also assumes that your "input" files are named exactly outputX.txt where X doesn't contain any whitespace.
Added by Mark Setchell... just for fun, the plots look kind of more professional if you label them a little bit, by adding the following:
...
out=...
# Echo the commands
echo set title \"${out} - plotted with gnuplot\"
echo set ylabel \"y axis\"
echo set xlabel \"x axis\"
I have been looking all around (with no avail) to perform the following:
I want to display and able to edit if necessary the content of a variable in runtime for a Unix shell script after giving it a value. The idea goes like this:
Suppose we have a variable value either defined in script or by user input
var=12345
Print the variable value, but also leave the cursor in that position of printing and either press just enter to leave it intact or enter a new value in runtime
Edit variable content (press Enter to leave intact) : 12345
at this point at runtime, I want to leave the cursor in the position of number 1, while showing the variable, and working in the way that if I press Enter, leave the original content (12345) or read for a new value in that same place and modify. Clearing the display of the variable when typing anything else than Enter would be a big plus.
I have looked all around for a way to do this, but just haven't found anything. Anyone willing to provide a solution?
I would suggest you doing this in another way:
var=12345
echo "Change the value of Var (current value: $var)"
read -p "New value (Press Enter to skip):" nvar
if [[ "$nvar" != "" ]]; then
var="$nvar"
fi
echo $var
with this, it will prompt:
Change the value of Var (current value: 12345)
New value (Press Enter to skip):
what you wanted in the question (without the "big plus" part), could be achieved too:
var=12345
echo -ne "Now you may want to change the value: \n$var\r"
read nvar
if [[ "$nvar" != "" ]]; then
var="$nvar"
fi
echo $var
with this, it will prompt (cursor sits between ** )
Now you may want to change the value:
*1*2345
With bash, you could use the readline option for read, but that does not put the cursor at the beginning. It does however do what you want
var=12345
read -ep "Enter new value: " -i $var var
If you need the cursor to go back, you can do this:
var=12345
prompt="Enter new value: $var"
for ((i=1; i<=${#var}; i++)); do prompt+=$'\b'; done
read -p "$prompt" new
[[ -z $new ]] && new=$var
This program I use has it's own variables to set when you run it, so I want to set those variables and then greping the output then storing it inside a variable. However, I don't know how to go about this the correct way. The idea I have doesn't work. The focus is on lines 7 through 14.
1 #!/usr/local/bin/bash
2 source /home/gempak/NAWIPS/Gemenviron.profile
3 FILENAME="$(date -u '+%Y%m%d')_sao.gem"
4 SFFILE="$GEMDATA/surface/$FILENAME"
5 echo -n "Enter the station ID: "
6 read -e STATION
7 OUTPUT=$(sflist << EOF
8 SFFILE = $SFFILE
9 AREA = #$STATION
10 DATTIM = all
11 SFPARM = TMPF;DWPF
12 run
13 exit
14 EOF)
15 echo $OUTPUT
But I get this:
./listweather: line 7: unexpected EOF while looking for matching `)'
./listweather: line 16: syntax error: unexpected end of file
Putting together everyone's answers, I came across a working solution myself. This code works for me:
#!/usr/local/bin/bash
source /home/gempak/NAWIPS/Gemenviron.profile
FILENAME="$(date -u '+%Y%m%d')_sao.gem"
SFFILE="$GEMDATA/surface/$FILENAME"
echo -n "Enter the station ID: "
read -e STATION
OUTPUT=$(sflist << EOF
SFFILE = $SFFILE
AREA = #$STATION
DATTIM = ALL
SFPARM = TMPF;DWPF
run
exit
EOF
)
echo $OUTPUT | grep $STATION
Thanks everyone!
I'd put your program to run in a separate .sh script file, and then run the script from your first file, passing the arguments you want to pass as command line arguments. That way you can test them separately.
You could also do it in a function, but I like the modularity of the second script. I don't udnerstand exactly what you are trying to do above, but something like:
runsflist.sh:
#!/bin/bash
FILENAME="$(date -u '+%Y%m%d')_sao.gem"
SFFILE="$GEMDATA/surface/$FILENAME"
AREA = #$STATION
DATTIM = all
SFPARM = TMPF;DWPF
grep $STATION | sflist
main.sh:
#!/bin/bash
echo -n "Enter the station ID: "
read -e STATION
OUTPUT=`runsflist.sh`
echo $OUTPUT
If sflist needs interaction, I'd try something like this:
SFFILE=$(
( echo SFFILE = "$SFFILE"
echo AREA = "#$STATION"
echo DATTIM = all
echo SFPARM = TMPF;DWPF
echo run
cat
) | sflist)
Unfortunately, you have to type exit as part of the interaction.