How to use loop statements in unix shell scripting for eg while ,for do while. I'm using putty server.
for: Iterate over a list.
$for i in `cat some_file | grep pattern`;do echo $i;done
while loop looks pretty much like C's.
$ i=0;while [ $i -le 10 ];do echo $i;i=`expr $i + 1` ;done
If you are going to use command line only, you could use perl, but I guess this is cheating.
$perl -e '$i=0;while ($i < 10){print $i;$i++;}'
More data
http://www.freeos.com/guides/lsst/
#!/bin/sh
items=(item1 item2 item3)
len=${#items[*]}
i=0
while [ $i -lt $len ]; do
echo ${items[$i]}
let i++
done
exit 0
As well as the 'for' and 'while' loops mentioned by Tom, there is (in classic Bourne and Korn shells at least, but also in Bash on MacOS X and presumably elsewhere too) an 'until' loop:
until [ -f /tmp/sentry.file ]
do
sleep 3
done
This loop terminates when the tested command succeeds, in contrast to the 'while' loop which terminates when the tested command fails.
Also note that you can test a sequence of commands; the last command is the one that counts:
while x=$(ls); [ -n "$x" ]
do
echo $x
done
This continues to echo all the files in the directory until they're all deleted.
to the OP, to iterate over files
for file in *
do
echo "$file"
done
to generate counters
for c in {0..10}
do
echo $c
done
using for loop
max=10
for (( i=0; i<=$max; i++ ));
do
echo $i
done
to iterate through a file in KSH
while read line ; do
echo "line from file $line"
done < filename.txt
echo "sample while loop"
i=0;
while [ $i -le 10 ]
do
echo $i
(( i++ ))
done
Related
I'm having a terrible go trying to pass some variables from the shell to R. I am hesitant to post this because I can't figure out a reasonable way to make this reproducible, since it involves a tool that has to be downloaded, and really it's more of a general methodology issue that I don't think needs to be reproducible, if you can just suspend your disbelief and bear with me for a quick minute.
I have arguments that are defined in a bash script: $P, $G, and $O.
I have some if/then statements and everything is fine until I get to the $O options.
This is the first part of the $O section and it works fine. It grabs data from $P and passes it to the twoBitToFa utility from UCSC's genome project and outputs the data correctly in a .fa file. Beautiful. (Although I think using 'stdout' and '>' is perhaps redundant?)
if [ "$O" = "fasta" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout > "${P%.bed}".fa
fi
The next section is where I am stuck. If the $O option is "bed", then I want to invoke the Rscript command and pass my stuff over to R. I am able to pass my $P, $G, and $O variables without issue, but now I also need to pass the output from the twoBitToFa function. I could add a step and make the .fa file and then pick that up in R, but I am trying to skip the .fa file creation step and output a different file type instead (.bed). Here are some things I have tried:
# try saving twoBitToFa output to variable and including it in the variables passed to R:
if [ "$O" = "bed" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
myvar=$(twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout) \
Rscript \
GetSeq_R.r \
$P \
$G \
$O \
$myvar
fi
To check what variables come through, my GetSeq_R.r script starts with:
args = commandArgs(trailingOnly=TRUE)
print(args)
and with the above code, the output only includes my $P, $G, and $O variables. $myvar doesn't make it. $P is the TAD-1 file, $G is "hg38", and $O is "bed".
[1] "TAD-1_template.bed" "hg38" "bed"
I am not sure if the way I am trying to pass the data in the variable is wrong. From everything I've read, it seems like it should work. I've also tried using tee to see what is in my stdout at that step like so:
if [ "$O" = "bed" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout | tee \
Rscript \
GetSeq_R.r \
$P \
$G \
$O
fi
And the data I want to pass to R is correctly shown in my console by using tee. I've tried saving stdout and tee to a variable and passing that variable to R, thinking maybe it's something about twoBitToFa that refuses to be put inside a variable, but was unsuccessful. I've spent hours looking up info about tee, stdout, and passing variables from bash to R. I feel like I'm missing something fundamental, or trying to do something impossible, and would really appreciate some other eyes on this.
Here's the whole bash script, in case that's illuminating. Do I need to define a variable in "$#" for what I am trying to pass to R, even though it's not something I want the user to be aware of? Am I capturing the variable with $myvar incorrectly? Can I get the contents of stdout or tee to show up in R?
Thanks in advance.
for arg in "$#"; do
shift
case "$arg" in
"--path") set -- "$#" "-P" ;;
"--genome") set -- "$#" "-G" ;;
"--output") set -- "$#" "-O" ;;
"--help") set -- "$#" "-h" ;;
*) set -- "$#" "$arg"
esac
done
while getopts ":P:G:O:h" OPT
do
case $OPT in
P) P=$OPTARG;;
G) G=$OPTARG;;
O) O=$OPTARG;;
h) help ;;
\?)
echo "Invalid option: -$OPTARG" >&2
usage
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
usage
exit 1
;;
esac
done
num_col=$(cat "$P" | awk "{print NF; exit}")
if [ "$num_col" = 3 ]
then
echo -e "\n\n3 column bed file detected; no directional considerations for sequences \n\n"
if [ "$G" = "hg38" ]
then
twobit="https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.2bit"
fi
if [ "$G" = "hg19" ]
then
twobit="https://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.2bit"
fi
if [ "$O" = "fasta" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout > "${P%.bed}".fa
fi
if [ "$O" = "bed" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
#myvar=$(twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout) \
Rscript \
GetSeq_R.r \
$P \
$G \
$O \
$myvar
fi
fi
I'm trying to execute a ksh where in the file it contains
a = 0
max = 25
while [[$a -ne $max]];
do
echo "$a"
a = $((a+5))
done
It's giving me an error
"[[0: not found [No such file or directory]"
I will check the while loop and it says 2 brackets are needs and ne is for numerical which I did.....I don't know why it is not working....
Try this code,
a=0
max=25
while [ $a -ne $max ]; #Changed here
do
echo "$a"
a=$((a+5))
done
For integers you can use
max=25
for (( a=0; a<max; a+=5 )); do
echo "a=$a"
done
Have two files:
file1 is having the key words - INFO ERROR
file2 is having the list of log files path - path1 path2
I need to exit out of the script if any of the condition in any of the loops failed.
Here is the Code:
#!/bin/bash
RC=0
while read line
do
echo "grepping from the file $line
if [ -f $line ]; then
while read key
do
echo "searching $key from the file $line
if [ condition ]; then
RC=0;
else
RC=1;
break;
fi
done < /apps/file1
else
RC=1;
break;
fi
done < apps/file2
exit $RC
Thank you!
The ansewer to your question is using break 2:
while true; do
sleep 1
echo "outer loop"
while true; do
echo "inner loop"
break 2
done
done
I never use this, it is terrible when you want to understand or modify the code.
Already better is using a boolean
found_master=
while [ -n "${found_master}" ]; do
sleep 1
echo "outer loop"
while true; do
echo "inner loop"
found_master=true
break
done
done
When you do not need the variable found_master it is an ugly additional variable.
You can use a function
inner_loop() {
local i=0;
while ((i++ < 5)); do
((random=$RANDOM%5))
echo "Inner $i: ${random}"
if [ ${random} -eq 0 ]; then
echo "Returning 0"
return 0
fi
done;
return 1;
}
j=0
while ((j++ < 5 )); do
echo "Out loop $j"
inner_loop
if [ $? -eq 0 ]; then
echo "inner look broken"
break
fi
done
But your original problem can be handles without two while loops.
You can use grep -E "INFO|ERROR" file2 or combining the keywords. When the keywords are on different lines in file1, you can use grep -f file1 file2.
Replace condition with $(grep -c ${key} ${line}) -gt 0 like this:
echo "searching $key from the file $line
if [ $(grep -c ${key} ${line}) -eq 0 ]; then
It will count the each key-word in your log-file. If count=0 (pattern didn't found), running then. If found at least 1 key, running else, RC=1 and exit from loop.
And be sure, that your key-words can't be substrings of the longest words, or you will get an error.
Example:
[sahaquiel#sahaquiel-PC Stackoverflow]$ cat file
correctstringERROR and more useless text
ERROR thats really error string
[sahaquiel#sahaquiel-PC Stackoverflow]$ grep -c ERROR file
2
If you wish to avoid count 2 (because counting first string, obliviously, bad way), you should also add two keys for grep:
[sahaquiel#sahaquiel-PC Stackoverflow]$ grep -cow ERROR file
1
Now you have counted only the words equal to your key, not substrings in any useful strings.
I'm trying to write a function to compare the versions of the products.
my versions can be XX.XX.XX or xx-xx-xx either it's separated with "." or "-"
and number of fields can be different either xx.xx or xx.xx.xx or xx.xx.xx.xx
the versions which im gonna compare will identical in delimiters and with the fields
#!/bin/ksh
set -x
compareVersions ()
{
typeset IFS='.'
typeset -a v1=( $1 )
typeset -a v2=( $2 )
typeset n diff
for (( n=0; n<4; n+=1 )); do
diff=$((v1[n]-v2[n]))
if [ $diff -ne 0 ] ; then
[ $diff -le 0 ] && echo '-1' || echo '1'
return
fi
done
echo '0'
} # ---------- end of function compareVersions ----------
#compareVersions "6100-09-03" "6100-09-02"
compareVersions "6100.09.03" "6100.09.02"
Please check and give me suggestions
I have tried with the below thing which i have got a other post.. but there is no luck.. hope there should some modification should be done. I have to use across platforms ( linux, solaris, AIX ) so i have preferred KSH, i have idea only in shell scripting though.
Create arrays from version strings, then loop through them comparing elements one by one and return values accordingly. The following example will compare two version strings and returns either 0 (versions are equal), 1 (the first version string is greater) or 2 (the second version string is greater).
#!/bin/ksh
function vertest {
set -A av1 `echo $1 | sed -e 's/\'$3'/ /g'`
set -A av2 `echo $2 | sed -e 's/\'$3'/ /g'`
for (( i=0; i < ${#av1[#]}; i++ )) ; do
[[ ${av1[$i]} -eq ${av2[$i]} ]] && continue
[[ ${av1[$i]} -gt ${av2[$i]} ]] && return 1
[[ ${av1[$i]} -lt ${av2[$i]} ]] && return 2
done
return 0
}
v1="2-7-2-1"
v2="1-8-0-1"
vertest $v1 $v2 '-'
exit $?
# end of file.
This example will exit to shell with exit code 1. Should you change $v1 to 1-7-2-1, it will exit to shell with exit code 2. And so on, and so forth.
The separator escaping is not complete, but this works with most reasonable separators like a period (.) and a dash (-). This, as well as parameter checking for the vertest() is left as an exercise for the reader.
When the format of both numbers is equal (leading zero as your example), you can use
compareVersions ()
{
val1=$(echo $1| tr -d ".-")
echo ${val1}
val2=$(echo $2| tr -d ".-")
echo ${val2}
if [ ${val1} -gt ${val2} ] ; then
echo 1
return
fi
if [ ${val1} -eq ${val2} ] ; then
echo 0
return
fi
echo '-1'
} # ---------- end of function compareVersions ----------
I just started writing shell scripts in Unix so, I am a total newbie
I want to read the arguments given when the user run the script
ex:
sh script -a abc
I want to read for argument -a user gave abc.
My code so far:
if ( $1 = "-a" )
then var=$2
fi
echo $var
I get an error.
Bash uses an external program called test to perform boolean tests, but that program is used mostly via its alias [.
if ( $1 = "-a" )
should become
if [ $1 = "-a" ]
if you use [ or
if test $1 = "-a"
#!/bin/sh
if [ $1 = "-a" ]; then
var=$2
fi
echo $var
You shoud be careful of the space between if and [