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 >$i.ab.out
but as question was changed I'm not sure to understand it.
Related
I have a large data file that contains many joint files.
It has an separate index file has that file name, start + end byte of each file within the data file.
I'm needing help in creating a bash script to split the large file into it's 1000's of sub files.
Data File : fileafilebfilec etc
Index File:
filename.png<0>3049
folder\filename2.png<3049>6136.
I guess this needs to loop through each line of the index file, then using dd to extract the relevant bytes into a file. Maybe a fiddly part might be the folder structure bracket being windows style rather than linux style.
Any help much appreciated.
while read p; do
q=${p#*<}
startbyte=${q%>*}
endbyte=${q#*>}
filename=${p%<*}
count=$(($endbyte - $startbyte))
toprint="processing $filename startbyte: $startbyte endbyte: $endbyte count: $c$
echo $toprint
done <indexfile
Worked it out :-) FYI:
while read p; do
#sort out variables
q=${p#*<}
startbyte=${q%>*}
endbyte=${q#*>}
filename=${p%<*}
count=$(($endbyte - $startbyte))
#let it know we're working
toprint="processing $filename startbyte: $startbyte endbyte: $endbyte count: $c$
echo $toprint
if [[ $filename == *"/"* ]]; then
echo "have found /"
directory=${filename%/*}
#if no directory exists, create it
if [ ! -d "$directory" ]; then
# Control will enter here if $directory doesn't exist.
echo "directory not found - creating one"
mkdir ~/etg/$directory
fi
fi
dd skip=$startbyte count=$count if=~/etg/largefile of=~/etg/$filename bs=1
done <indexfile
I want all variables names are set in shell script. I have a file which contains key value pairs and I was read content from that file and store/set into variables. I want to do some processes if a variable is available/set otherwise I don't need to do those processes. How to achieve this.
For example I run loop in shell scripts in each iteration it gives one of the variables is set before that command.
If code like this
a=test1
b=test2
c=test3
for i in ???
do
echo $i
done
then I want output like this
a
b
c
What command is used o achieve this.
You could use set before and after setting the variables
e.g:
$ set > aux1
$ c=345
$ set > aux2
$ diff aux1 aux2
57c57
< PIPESTATUS=([0]="141" [1]="0")
---
> PIPESTATUS=([0]="0")
112a113
> c=345
If you have a pre-defined list of such variables, then you can test it like this:
for i in $(echo "a b c"); do
echo $i
done
If i could help you :
#!/bin/sh
# Define list of tests
LIST_TESTS=`cat list_test.txt`
for TEST in ${LIST_TESTS}
do
vartest=`echo ${TEST}`
if [ "${vartest}" = "" ]
# No Test
then
echo "*** WARNING*** Test not found"
else
echo "${vartest} is available"
fi
done
# Second Define list of tests
tabTest=('test1' 'test2' 'test3')
i=0
while [ "${tabTest[$i]}" != "" ]
do
echo "${tabTest[$i]} is available"
i=$(($i+1))
done
on Android Linux - I want to assign a var to a date value - but I can't figure out how to get (Busybox?) the shell to not return 0 for my desired format.
let hourfiletag="$(date +%j%H)"
echo $hourfiletag
let tagtwo="D$hourfiletag"
echo $tagtwo
let tagthree="D${hourfiletag}H"
echo $tagthree
let hourfiletag="$(date +D%jH%H)"
echo $hourfiletag
let tagtwo="D$hourfiletag"
echo $tagtwo
let tagthree="D${hourfiletag}H"
echo $tagthree
When I run this, here is the output I get:
$ ./date1.sh
34011
0
0
0
0
0
The date command can produce exactly what I want:
$ date +D%jH%H
D340H11
But I am unable to make it a variable that I can use in a file cp operation. Thank you.
let is used to Evaluate arithmetic expressions
You can just use:
hourfiletag=`date '+D%jH%H'`
OR:
hourfiletag=$(date '+D%jH%H')
echo "$hourfiletag"
D340H12
No need let at all :
$ cat a
hourfiletag="$(date +%j%H)"
echo $hourfiletag
tagtwo="D$hourfiletag"
echo $tagtwo
tagthree="D${hourfiletag}H"
echo $tagthree
hourfiletag="$(date +D%jH%H)"
echo $hourfiletag
tagtwo="D$hourfiletag"
echo $tagtwo
tagthree="D${hourfiletag}H"
echo $tagthree
Output:
shell#android:/ $ sh /storage/sdcard0/a
34018
D34018
D34018H
D340H18
DD340H18
DD340H18H
I created a bash script that parses ASCII files into a comma delimited output. It's worked great. Now, a new file layout for these files is being gradually introduced.
My script has now two parsing functions (one per layout) that I want to call depending on a specific marker that is present in the ASCII file header. The script is structured thusly:
#!/bin/bash
function parseNewfile() {...parse stuff...return stuff...}
function parseOldfile() {...parse stuff...return stuff...}
#loop thru ASCII files array
i=0
while [ $i -lt $len ]; do
#check if file contains marker for new layout
grep CSVHeaderBox output_$i.ASC
#calls parsing function based on exit code
if [ $? -eq 0 ]
then
CXD=`parseNewfile`
else
CXD=`parseOldfile`
fi
echo ${array[$i]}| awk -v cxd=`echo $CXD` ....
let i++
done>>${outdir}/outfile.csv
...
The script does not err out. It always calls the original function "parseOldfile" and ignores the new one. Even when I specifically feed my script with several files with the new layout.
What I am trying to do seem very trivial. What am I missing here?
EDIT: Samples of old and new file layouts.
1) OLD File Layout
F779250B
=====BOX INFORMATION=====
Model = R15-100
Man Date = 07/17/2002
BIST Version = 3.77
SW Version = 0x122D
SW Name = v1b1645
HW Version = 1.1
Receiver ID = 00089787556
=====DISK INFORMATION=====
....
2) NEW File Layout
F779250B
=====BOX INFORMATION=====
Model = HR22-100
Man Date = 07/17/2008
BIST Version = 7.55
SW Version = 0x066D
SW Name = v18m1fgu
HW Version = 2.3
Receiver ID = 028910170936
CSVHeaderBox:Platform,ManufactureDate,BISTVersion,SWVersion,SWName,HWRevision,RID
CSVValuesBox:HR22-100,20080717,7.55,0x66D,v18m1fgu,2.3,028910170936
=====DISK INFORMATION=====
....
This may not solve your problem, but a potential performance boost: instead of
grep CSVHeaderBox output_$i.ASC
#calls parsing function based on exit code
if [ $? -eq 0 ]
use
if grep -q CSVHeaderBox output_$i.ASC
qrep -q will exit successfully on the first match, so it doesn't have to scan the whole file. Plus you don't have to bother with the $? var.
Don't do this:
awk -v cxd=`echo $CXD`
Do this:
awk -v cxd="$CXD"
I'm not sure if this solves the OP's requirement.
What's the need for awk if your function knows how to parse the file?
#/bin/bash
function f1() {
echo "f1() says $#"
}
function f2() {
echo "f2() says $#"
}
FUN="f1"
${FUN} "foo"
FUN="f2"
${FUN} "bar"
I am bit embarrassed to write this but I solved my "problem".
After gedit (I am on Ubuntu) err-ed out several dozen times about "Trailing spaces", I copied and pasted my code into a new file and re-run my script.
It worked.
I have no explanation why.
Thanks to everyone for taking the time.
This program I use has it's own variables to set when you run it, so I want to set those variables and then greping the output then storing it inside a variable. However, I don't know how to go about this the correct way. The idea I have doesn't work. The focus is on lines 7 through 14.
1 #!/usr/local/bin/bash
2 source /home/gempak/NAWIPS/Gemenviron.profile
3 FILENAME="$(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.