I am trying to use the following command to extract a substring from a string :
propertyPath=$(echo $path|awk '{print substr($0,3,$index)}')
However the command does not pick up the value of the $index variable and therefore does not return a valid substring.
This would work:
propertyPath=$(echo $path|awk '{print substr($0,3,'$index')}')
or
propertyPath=$(echo $path|awk -v index=$index '{print substr($0,3,index)}')
propertyPath=$(echo $path|awk "{print substr(\$0,1,$index)}")
Single quotes tell the shell not to expand values, so you'll have to use double quotes around your awk command. When you do that though, you'll have to escape the $ for the variables you do not want to expand early.
Related
I am trying to run bioawk (an extension of awk for fasta files) from awk's system functionality:
awk -v var=$i '{system("~/bin/bioawk-master/bioawk -c fastx '\''{if ($name==\""var"\"){print \">\"$name\"\\\\n\"$seq}}'\'' ../../prokka/"$2"/"$1"/"$1".ffn")}'
The result prints the literal "\n" between the values of $name and $seq instead of the intended carriage return.
What it prints:
NAME\nSEQUENCE
What I would like it to print:
NAME
SEQUENCE
When I print the bioawk command that want to run with:
awk -v var=$i '{system("echo ~/bin/bioawk-master/bioawk -c fastx '\''{if ($name==\""var"\"){print \">\"$name\"\\\\n\"$seq}}'\'' ../../prokka/"$2"/"$1"/"$1".ffn")}'
I get:
~/bin/bioawk-master/bioawk -c fastx {if ($name=="CANHHJNM_03494"){print ">"$name"\n"$seq}} ../../prokka/p190631-dr-tm-dc-sp-pi/EP41/EP41.ffn
I can see that it is missing the single quotes surrounding the brackets. I though having '\'' would solve this issue, but obviously it doesn't. Any help with this problem would be much appreciated
not sure this will solve your problem but the (second) easiest way to handle single quotes in an awk script is defining it externally as a variable
$ awk -v q="'" 'BEGIN{print q "single_quoted" q}'
'single_quoted'
I'm trying to figure out a command to parse the following file content:
Operation=GET
Type=HOME
Counters=CacheHit=0,Exception=1,Validated=0
I need to extract Exception=1 into its own line. I'm fiddling with awk, sed and grep but not making much progress. Does anyone have any tips on using any unix command to perform this?
Thanks
Since your file is close to bash syntax, there is a fun little trick you can do to make bash itself parse the file. First, use some program like tr to transform the input into a something bash can parse, and then "source" that, which will create shell variables you can expand later to get the values.
source <(tr , $'\n' < file_name_goes_here)
echo $Exception
Many ways to do this. Here is one assuming the file is called "file.txt". Grab the line you want, replace everything from the start of the line up to Except with just Except, then pull out the first field using comma as the delimiter.
$ grep Exception file.txt | sed 's/.*Except/Except/g' | cut -d, -f 1
Exception=1
If you wanted to use gawk:
$ grep Exception file.txt | sed 's/.*Except/Except/g' | gawk -F, '{print $1}'
Exception=1
or just using grep and sed:
$ grep Exception file.txt | sed 's/.*\(Exception=[0-9]*\).*/\1/g'
Exception=1
or as #sheltter reminded me:
$ egrep -o "Exception=[0-9]+" file.txt
Exception=1
No need to use a mix of commands.
awk -F, 'NR==2 {print RS$1}' RS="Exception" file
Exception=1
Here we split the line by the keyword we look for RS="Exception"
If the line has two record (only when keyword is found), then
print first field, separated using command, with Record selector.
PS This only works if you have one Exception field
How to use "grep" shell command to show specific word from a line starting with a specific word.
Ex:
I want to print a string "myFTPpath/folderName/" from the line starting with searchStr in the below mentioned line.
searchStr:somestring:myFTPpath/folderName/:somestring
Something like this with awk:
awk -F: '/^searchStr/{print $3}' File
From all the lines starting with searchStr, print the 3rd field (field seperator set as :)
Sample:
AMD$ cat File
someStr:somestring:myFTPpath/folderName/:somestring
someStr:somestring:myFTPpath/folderName/:somestring
searchStr:somestring:myFTPpath/folderName/:somestring
someStr:somestring:myFTPpath/folderName/:somestring
AMD$ awk -F: '/^searchStr/{print $3}' File
myFTPpath/folderName/
Remember that grep isn't the only tool that can usefully do searches.
In this particular case, where the lines are naturally broken into fields, awk is probably the best solution, as #A.M.D's answer suggests.
For more general case edits, however, remember sed's -n option, which suppresses printing out a line after edits:
sed -n 's/searchStr:[^:]*:\([^:]*\):.*/\1/p' input-file
The -n suppresses automatic printing of the line, and the trailing /p flag explicitly prints out lines on which there is a substitution.
This matching pattern is fiddly – use awk in this fielded case – but don't forget sed -n.
You could get the desired output with grep itself but you need to enable -P and -o parameters.
$ echo 'searchStr:somestring:myFTPpath/folderName/:somestring' | grep -oP '^searchStr:[^:]*:\K[^:]*'
myFTPpath/folderName/
\K discards the characters which are matched previously from printing at the final leaving only the characters which are matched by the pattern exists next to \K. Here we used \K instead of a variable length positive lookbehind assertion.
Eg- lets suppose I want to grep string VR030315ITVENDMXN. Then grep should not show VR030315ITVENDMXN-LPP or any additional things with VR030315ITVENDMXN .
Can you use anchors?
For instance:
grep '^VR030315ITVENDMXN$' file
There is a similar question here How to make grep only match if the entire line matches?
You need to use the -o (or --only-matching ) option in your command line option
Of you do not desire to have the filename displayed use the -h (--no-filename) option in addition to remove them.
I have a log file (application.log) which might contain the following string of normal & special characters on multiple lines:
*^%Q&$*&^#$&*!^#$*&^&^*&^&
I want to search for the line number(s) which contains this special character string.
grep '*^%Q&$*&^#$&*!^#$*&^&^*&^&' application.log
The above command doesn't return any results.
What would be the correct syntax to get the line numbers?
Tell grep to treat your input as fixed string using -F option.
grep -F '*^%Q&$*&^#$&*!^#$*&^&^*&^&' application.log
Option -n is required to get the line number,
grep -Fn '*^%Q&$*&^#$&*!^#$*&^&^*&^&' application.log
The one that worked for me is:
grep -e '->'
The -e means that the next argument is the pattern, and won't be interpreted as an argument.
From: http://www.linuxquestions.org/questions/programming-9/how-to-grep-for-string-769460/
A related note
To grep for carriage return, namely the \r character, or 0x0d, we can do this:
grep -F $'\r' application.log
Alternatively, use printf, or echo, for POSIX compatibility
grep -F "$(printf '\r')" application.log
And we can use hexdump, or less to see the result:
$ printf "a\rb" | grep -F $'\r' | hexdump -c
0000000 a \r b \n
Regarding the use of $'\r' and other supported characters, see Bash Manual > ANSI-C Quoting:
Words of the form $'string' are treated specially. The word expands to string, with backslash-escaped characters replaced as specified by the ANSI C standard
grep -n "\*\^\%\Q\&\$\&\^\#\$\&\!\^\#\$\&\^\&\^\&\^\&" test.log
1:*^%Q&$&^#$&!^#$&^&^&^&
8:*^%Q&$&^#$&!^#$&^&^&^&
14:*^%Q&$&^#$&!^#$&^&^&^&
You could try removing any alphanumeric characters and space. And then use -n will give you the line number. Try following:
grep -vn "^[a-zA-Z0-9 ]*$" application.log
Try vi with the -b option, this will show special end of line characters
(I typically use it to see windows line endings in a txt file on a unix OS)
But if you want a scripted solution obviously vi wont work so you can try the -f or -e options with grep and pipe the result into sed or awk.
From grep man page:
Matcher Selection
-E, --extended-regexp
Interpret PATTERN as an extended regular expression (ERE, see below). (-E is specified by POSIX.)
-F, --fixed-strings
Interpret PATTERN as a list of fixed strings, separated by newlines, any of which is to be matched. (-F is specified
by POSIX.)