Im trying to make a script that takes a .txt file containing lines
like:
davda103:David:Davidsson:800104-1234:TNCCC_1:TDDB46 TDDB80:
and then sort them etc. Thats just the background my problem lies here:
#!/bin/sh -x
cat $1 |
while read a
do
testsak = `echo $a | cut -f 1 -d :`; <---**
echo $testsak;
done
Where the arrow is, when I try to run this code I get some kind of weird error.
+ read a
+ cut -f+ echo 1 -d :davda103:David:Davidsson:800104-1234:TNCCC_1:TDDB46
TDDB80:
+ testsak = davda103
scriptTest.sh: testsak: Det går inte att hitta
+ echo
(I have my linux in swedish because school -.-) Anyways that error just says that it cant find... something. Any ideas what could be causing my problem?
You have extra spaces around the assignment operator, remove them:
testsak=`echo $a | cut -f 1 -d :`; <---**
The spaces around the equal sign
testsak = `echo $a | cut -f 1 -d :`; <---**
causes bash to interpret this as a command testak with arguments = and the result of the command substitution. Removing the spaces will fix the immediate error.
A much more efficient way to extract the value from a is to let read do it (and use input redirection instead of cat):
while IFS=: read testak the_rest; do
echo $testak
done < "$1"
Related
I am trying to extract two #define values from a C header file to use them in a shell script. So I use grep to find them and then print them. However, the variables are sometimes empty.
// main.h
#define DEVICE_NO 1
#define FW_VERSION 1
And the script file is
#!/bin/bash -
read_version()
{
echo $(grep $1 "$projectdir/Inc/main.h" | cut -d ' ' -f 3-)
}
device_no=$(read_version "DEVICE_NO")
fw_version=$(read_version "FW_VERSION")
echo "DEVICE_NO = $device_no, FW_VERSION = $fw_version"
So the expectation is that the output to be:
DEVICE_NO = 1, FW_VERSION = 1
but sometimes it turns to be
5
DEVICE_NO = , FW_VERSION = 1
It randomly misses one or both of the values. The header file does not change so it's not coming from there.
UPDATE
As commented I thought maybe the windows line ending is a problem so I piped the output to tr and removed \r but it did not make any difference. also tried var=$(grep FW_VERSION file); $(echo ${var//[$'\t\r\n']} | cut ... to no avail.
I tried using awk instead of cut but got the same result.
I redirected the error inside the command to the standard output ($(grep $1 file | cut -d ' ' -f 3 2>&1) but did not get any extra information
I split the command to a grep part and a cut, the grep never misses but the output of cut randomly gives an empty string as output.
I still have no idea where that 5 is coming from, there is nothing in cut or awk manuals that throws a 5 to either standard output or stderr.
I need to write bash script that converts a string of only integers "intString" to :id. intString always exists after /, may never contain any other types (create_step2 is not a valid intString), and may end at either a second / or end of line. intString may be any 1-8 characters. Script needs to be repeated for every line in a given file.
For example:
/sample/123456/url should be converted to /sample/:id/url
and /sample_url/9 should be converted to /sampleurl/:id however /sample_url_2/ should remain the same.
Any help would be appreciated!
It seems like the long way around the problem to go recursive but then I don't know what problem you are solving. It seems like a good sed command like
sed -E 's/\/[0-9]{1,}/\/:id/g'
could do it in one shot, but if you insist on being recursive then it might go something like this ...
#!/bin/bash
function restring()
{
s="$1"
s="$(echo $s | sed -E 's/\/[0-9]{1,}/\/:id/')"
if ( echo $s | grep -E '\/[0-9]{1,}' > /dev/null ) ; then
restring $s
else
echo $s
exit
fi
echo $s
}
restring "$1"
now run it
$ ./restring.sh "/foo/123/bar/456/baz/45435/andstuff"
/foo/:id/bar/:id/baz/:id/andstuff
shell script to print three words differently I have tried
{
a="Uname/pass#last"
echo $a | tr "/" "\n" | tr "#" "\n"
output is:
Uname
pass
last
}
I want it as
{Username- Uname
Password- pass
lastname-last}
Ok, I guess you want to add a prefix to each results:
printf 'Username\nPassword\nlastname' > /tmp/prefixes
a="Uname/pass#last"
echo "${a}" | tr '/#' '\n\n' | paste -d':' /tmp/prefixes -
ie: paste together the output of /tmp/prefixes and of the Standard Input (-), which is receiving the output of : echo ".../...#..." | tr '/#' '\n\n'
(and in the resulting output, separate the 2 with a : in this example, or whatever else you would want. Ex: - like in your question.)
and it outputs :
Username:user
Password:pass
lastname:last
(I know you wanted a - instead of a : but I give my example with : to better separate the "-" denoting the standard input, and the ":" denoting the field-separator character in the output. Just change -d':' into -d'-' to have a - instead.)
First off, I hope you're not going to manipulate important passwords in a shell script and external commands. There are some risks involved with that.
Defining the problem
I suspect you want split a string encoding a user's Username, password and surname into a three line structure, adding tags to document which is which. For that, tr is insufficient.
However, it can be done inside the shell.
Example (bash, ksh):
function split_account_string {
typeset account=${1:?account string} uname pass last t
uname=${account%%/*}
last=${account##*#}
t=${account#$uname/}
pass=${t%#*}
[[ $uname/$pass#$last == "$account" ]] || return
echo "{Username-$uname"
echo "Password-$pass"
echo "lastname-$last}"
}
split_account_string "USER_A/seKreT#John.Doe"
This function will extract all tokens between the first / and the last # as the value of the password. If either one is missing, it will print nothing, and return an error status.
When run, this gives:
{Username-USER_A
Password-seKreT
lastname-John.Doe}
Use this simple script and get the output.
#!/bin/bash
a="Uname/pass#last"
array2=(`echo $a | tr "/" "\n" | tr "#" "\n"`)
array1=(`echo -e "Username\nPassword\nlastname"`)
i=${#array1[#]}
for (( j=0 ; j<$i ; j++ ))
do
echo "${array1[$j]}=${array2[$j]}"
done
**Edit: Okay, so I've tried implementing everyone's advice so far.
-I've added quotes around each variable "$1" and "$codon" to avoid whitespace.
-I've added the -ioc flag to grep to avoid caps.
-I tried using tr -d' ', however that leads to a runtime error because it says -d' ' is an invalid option.
Unfortunately I am still seeing the same problem. Or a different problem, which is that it tells me that every codon appears exactly once. Which is a different kind of wrong.
Thanks for everything so far - I'm still open to new ideas. I've updated my code below.**
I have this bash script that is supposed to count all permutations of (A C G T) in a given file.
One line of the script is not giving me the desired result and I don't know why - especially because I can enter the exact same line of code in the command prompt and get the desired result.
The line, executed in the command prompt, is:
cat dnafile | grep -o GCT | wc -l
This line tells me how many times the regular expression "GCT" appears in the file dnafile. When I run this command the result I get is 10 (which is accurate).
In the code itself, I run a modified version of the same command:
cat $1 | grep -o $codon | wc -l
Where $1 is the file name, and $codon is the 3-letter combination. When I run this from within the program, the answer I get is ALWAYS 0 (which is decidedly not accurate).
I was hoping one of you fine gents could enlighten this lost soul as to why this is not working as expected.
Thank you very, very much!
My code:
#!/bin/bash
#countcodons <dnafile> counts occurances of each codon in sequence contained within <dnafile>
if [[ $# != 1 ]]
then echo "Format is: countcodons <dnafile>"
exit
fi
nucleos=(a c g t)
allCods=()
#mix and match nucleotides to create all codons
for x in {0..3}
do
for y in {0..3}
do
for z in {0..3}
do
perm=${nucleos[$x]}${nucleos[$y]}${nucleos[$z]}
allCods=("${allCods[#]}" "$perm")
done
done
done
#for each codon, use grep to count # of occurances in file
len=${#allCods[*]}
for (( n=0; n<len; n++ ))
do
codon=${allCods[$n]}
occs=`cat "$1" | grep -ioc "$codon" | wc -l`
echo "$codon appears: $occs"
# if (( $occs > 0 ))
# then
# echo "$codon : $occs"
# fi
done
exit
You're generating your sequences in lowercase. Your code greps for gct, not GCT. You want to add the -i switch to grep. Try:
occs=`grep -ioc $codon $1`
You've got your logic backwards - you shouldn't have to read your input file once for every codon, you should only have to read it once and check each line for every codon.
You didn't supply any sample input or expected output so it's untested but something like this is the right approach:
awk '
BEGIN {
nucleosStr="a c g t"
split(nucleosStr,nucleos)
#mix and match nucleotides to create all codons
for (x in nucleos) {
for (y in nucleos) {
for (z in nucleos) {
perm = nucleos[x] nucleos[y] nucleos[z]
allCodsStr = allCodsStr (allCodsStr?" ":"") perm
}
}
}
split(allCodsStr,allCods)
}
{
#for each codon, count # of occurances in file
for (n in allCods) {
codon = allCods[n]
if ( tolower($0) ~ codon ) {
occs[n]++
}
}
}
END {
for (n in allCods) {
printf "%s appears: %d\n", allCods[n], occs[n]
}
}
' "$1"
I expect you'll see a huge performance improvement with that approach if your file is moderately large.
Try:
occs=`cat $1 | grep -o $codon | wc -l | tr -d ' '`
The problem is that wc indents the output, so $occs has a bunch of spaces at the beginning.
Asking a question here is always my last resort. I tried everything even the most embarrassing code so i'm confused on explaining what i tried with no success. I have:
echo $output | grep -i -m 1 "Time:" | sed 's/.*\s\([0-9]*:[0-9]*:[0-9]*\).time.*/\1/'
it outputs:
23:25:31
Easy.
But i'd like to add one more string to the end, like " , $year" - so that i have:
23:25:31 , 2013
The problem is that whatever i tried (printf, -n, -e, -ne, brackets, quotes, |, ;, &, /r, etc.) gives an error or goes to a new line anyway.
Any suggestion will be really appreciated.
Thanks
time=$(echo $output | grep -i -m 1 "Time:" | sed 's/.*\s\([0-9]*:[0-9]*:[0-9]*\).time.*/\1/')
echo "The time is ${time}, 2013"
Alternates
add tr -d '\n' at the end of echo+grep+sed pipeline.
{ entire-echo-grep-sed-pipeline ; echo , 2013 ; } | xargs echo (This however, will add a space before ,)