Split a line after single quote into a newline - awk

I have a text file like this
'ABC&\]D' 'DEFGH' 'QUEMKLEMEL' 'SSBJ|!KFFL'
and would like to convert it to
'ABC&\]D'
'DEFGH'
'QUEMKLEMEL'
'SSBJ|!KFFL'
to split the textfile at the single quotes into a newline.
The original issue is to convert a bash script from windows (the EOL characters to Unix format). I tried
sed 's/\r//' input >output
but keep getting the error when I submit the script
sbatch: error: This does not look like a batch script.
It is a long text file from windows that was transferred to linux but does not work because of the EOL characters. I tried other options to convert it so thought can subset the issue, and try it this way.

Using GNU awk for it:
$ gawk -v FPAT="([^ ]+)|('[^']+')" -v OFS="\n" '{$1=$1}1' file
Output
'ABC&\]D'
'DEFGH'
'QUEMKLEMEL'
'SSBJ|!KFFL'

Using gnu sed you can search for "' " and replace with \n:
sed "s/' /'\n/g" file
'ABC&\]D'
'DEFGH'
'QUEMKLEMEL'
'SSBJ|!KFFL'
Or using POSIX awk:
awk '{gsub(/\x27 /, "\x27\n")} 1' file
'ABC&\]D'
'DEFGH'
'QUEMKLEMEL'
'SSBJ|!KFFL'
or this one:
awk -F "' " -v OFS="'\n" '{$1=$1} 1' file

1st solution: Using gsub function of awk.
awk '{gsub(/\x27 \x27/,"\x27\n\x27")} 1' Input_file
2nd solution: Could you please try following, written and tested with shown samples.
awk '{for(i=1;i<=NF;i++){print $i}}' Input_file

Related

spacial character replacement using sed or awk

I have a string in a dat file
Times-New $\Gamma$
and I want to replace it using sed or awk (I would prefer to use awk) utility with
/Symbol G
I could replace only one $ sign but failed for the remaining text.
So what I want is
sed 's/Times-New $\Gamma$/Symbol G/g' case.dat
Could you please help me?
Could you please try following, written and tested with shown samples. We need to escape \ and $ to make awk treat them as a literal character in program.
awk '{gsub(/Times-New \$\\Gamma\$/,"/Symbol G")} 1' Input_file
OR as per OP's comment try(Thanks to anubhava sir for adding solution):
awk '{gsub(/Times-New[ \t]+(G|\$\\Gamma\$)/, "/Symbol G")} 1' Input_file
With GNU sed try:
sed -E 's/Times-New \$\\Gamma\$/Symbol G/g' Input_file

awk set command line options in script

I'm curious about how to set command-line options in awk script, like -F for field separator. I try to write the shebang line like
#!/usr/bin/awk -F ":" -f
and get the following error:
awk: 1: unexpected character '.'
For this example, I can do with
BEGIN {FS=":"}
but I still want to know a way to set all those options. Thanks in advance.
EDIT:
let's use another example that should be easy to test.
inputfile:
1
2
3
4
test.awk:
#!/usr/bin/awk -d -f
{num += $1}
END { print num}
run
/usr/bin/awk -d -f test.awk inputfile
will get 10 and generate a file called awkvars.out with some awk global variables in it.
but
./test.awk inputfile
will get
awk: cmd. line:1: ./test.awk
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: ./test.awk
awk: cmd. line:1: ^ unterminated regexp
if I remove '-d' from shebang line,
./test.awk inputfile
will normally output 10.
My question is that whether there is a way to write "-d" in test.awk file to generate awkvars.out file?
Answering for the OP question, beyond the setting of FS.
Short Answer: you can not use multiple options with '#!', and since you need to tell awk to read the program from stdin (-f-), you are out of luck.
Long Answer:
When using shebang (#!), there is a limit of single argument (which is passed to the named programs as the 1st argument. So in general:
#! /path/to/prog arg1
input-1
input-2
Will execute /path/to/prog arg1, with the content of the file (including the leading shebang) available as stdin. This is oversimplification, actual rules are more complex., see https://unix.stackexchange.com/questions/87560/does-the-shebang-determine-the-shell-which-runs-the-script
Given this limitation of one argument, when executing awk, the only valid and required parameter is '-f', which indicates that the awk programs is provided on STDIN. You can prepend few other options that do NOT take any argument, for example 'traditional' (e.g., '-Pf-' will force POSIX behavior).
As much as I can tell, all the 'interesting' options (setting FS, RS, ORS, ...) need to be separated from the '-f-' with a space, making it impossible to embed them into the command line, other then using the 'BEGIN { ... }' or similar in the script.
Bottom line, trying #! /usr/bin/awk -f- -F, will attempt to look for program is the same as awk -f' -F', and will look for a file named '- -F`. Usually not very useful, and will not set the FS.
Let's say following is our Input_file, which we are going to use for all mentioned solutions here.
cat Input_file
a,b,c,d
ab,c
1st way of setting Field separator: 1st simple way will be setting FS value in BEGIN section of awk program file. Following is our .awk file.
cat file1.awk
BEGIN{
FS=","
}
{
print $1"..."$2
}
Now when we run the code following output will come:
/usr/local/bin/awk -f file1.awk Input_file
a...b
ab...c
2nd way of setting field separator: 2nd way will be pass FS value before reading Input_file like as follows.
/usr/local/bin/awk -f file.awk FS="," Input_file
Example: Now following is the file.awk file which has awk code.
cat file.awk
{
print $1".."$2
}
Now when we run awk file with awk -f .. command as follows will be result.
/usr/local/bin/awk -f file.awk FS="," Input_file
a..b
ab..c
Which means it is picking up the field separator as , in this above program.
3rd way of setting field separator: We can set field separator in awk -f programs like how we do for usual awk programs using -F',' option as follows.
/usr/local/bin/awk -F',' -f file.awk Input_file
a..b
ab..c
4th way of setting field separator: We could mention field separator as a variable by using -v option on command line while running file.awk script as follows.
/usr/local/bin/awk -v FS=',' -f file.awk Input_file
Never use a shebang to call awk as it robs you of the ability to separate shell arguments into awk arguments and awk variables and do anything else that's better done in shell (e.g. arg parsing with getopts) before calling awk. Just call awk from inside your shell script.
Also, don't name your shell script test.awk as it's a shell script. The fact it's implemented in awk is irrelevant. There's no reason to create a file that you sometimes call as awk file to have awk interpret and other times as just file to have the shell interpret.

Grep part of string after symbol and shuffle columns

I would like to take the number after the - sign and put is as column 2 in my matrix. I know how to grep the string but not how to print it after the text string.
in:
1-967764 GGCTGGTCCGATGGTAGTGGGTTATCAGAACT
3-425354 GCATTGGTGGTTCAGTGGTAGAATTCTCGCC
4-376323 GGCTGGTCCGATGGTAGTGGGTTATCAGAAC
5-221398 GGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCT
6-180339 TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCT
out:
GGCTGGTCCGATGGTAGTGGGTTATCAGAACT 967764
GCATTGGTGGTTCAGTGGTAGAATTCTCGCC 425354
GGCTGGTCCGATGGTAGTGGGTTATCAGAAC 376323
GGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCT 221398
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCT 180339
awk -F'[[:space:]-]+' '{print $3,$2}' file
Seems like a simple substitution should do the job:
sed -E 's/[0-9]+-([0-9]+)[[:space:]]*(.*)/\2 \1/' file
Capture the parts you're interested in and use them in the replacement.
Alternatively, using awk:
awk 'sub(/^[0-9]+-/, "") { print $2, $1 }' file
Remove the leading digits and - from the start of the line. When this is successful, sub returns true, so the action is performed, printing the second field, followed by the first.
Using regex ( +|-) as field separator:
$ awk -F"( +|-)" '{print $3,$2}' file
GGCTGGTCCGATGGTAGTGGGTTATCAGAACT 967764
GCATTGGTGGTTCAGTGGTAGAATTCTCGCC 425354
GGCTGGTCCGATGGTAGTGGGTTATCAGAAC 376323
GGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCT 221398
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCT 180339
here is another awk
$ awk 'split($1,a,"-") {print $2,a[2]}' file
awk '{sub(/.-/,"");print $2,$1}' file
GGCTGGTCCGATGGTAGTGGGTTATCAGAACT 967764
GCATTGGTGGTTCAGTGGTAGAATTCTCGCC 425354
GGCTGGTCCGATGGTAGTGGGTTATCAGAAC 376323
GGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCT 221398
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCT 180339

How do i delete all the lines in a file ending with colon using awk or sed?

I have a file with some tabular data in it. But it also has some text line(ending with a colon) in between the data. So i want to remove those text lines and only have my data.
Try this:
awk '{gsub(/:$/,""); print}' file.txt
This will take only the last colon and not the one which contain colon in between the line.
or as JID commented:
awk '!/:$/' file
you could use grep - something like
grep -v ":$" file
or sed - like
sed "/:$/d" file

awk to transpose lines of a text file

A .csv file that has lines like this:
20111205 010016287,1.236220,1.236440
It needs to read like this:
20111205 01:00:16.287,1.236220,1.236440
How do I do this in awk? Experimenting, I got this far. I need to do it in two passes I think. One sub to read the date&time field, and the next to change it.
awk -F, '{print;x=$1;sub(/.*=/,"",$1);}' data.csv
Use that awk command:
echo "20111205 010016287,1.236220,1.236440" | \
awk -F[\ \,] '{printf "%s %s:%s:%s.%s,%s,%s\n", \
$1,substr($2,1,2),substr($2,3,2),substr($2,5,2),substr($2,7,3),$3,$4}'
Explanation:
-F[\ \,]: sets the delimiter to space and ,
printf "%s %s:%s:%s.%s,%s,%s\n": format the output
substr($2,0,3): cuts the second firls ($2) in the desired pieces
Or use that sed command:
echo "20111205 010016287,1.236220,1.236440" | \
sed 's/\([0-9]\{8\}\) \([0-9]\{2\}\)\([0-9]\{2\}\)\([0-9]\{2\}\)\([0-9]\{3\}\)/\1 \2:\3:\4.\5/g'
Explanation:
[0-9]\{8\}: first match a 8-digit pattern and save it as \1
[0-9]\{2\}...: after a space match 3 times a 2-digit pattern and save them to \2, \3 and \4
[0-9]\{3\}: and at last match 3-digit pattern and save it as \5
\1 \2:\3:\4.\5: format the output
sed is better suited to this job since it's a simple substitution on single lines:
$ sed -r 's/( ..)(..)(..)/\1:\2:\3./' file
20111205 01:00:16.287,1.236220,1.236440
but if you prefer here's GNU awk with gensub():
$ awk '{print gensub(/( ..)(..)(..)/,"\\1:\\2:\\3.","")}' file
20111205 01:00:16.287,1.236220,1.236440