How to append string with special characters to each line using AWK - awk

I have a csv and for each line in the csv, I need to add new columns. One of the columns is a timestamp and it seems to be breaking the operation.
Example:
col1,col2,col3
1,2,3
4,5,7
After
col1,col2,col3,col4,col5,col6
1,2,3,01-01-2020 01:01:01,name,class
4,5,7,01-01-2020 01:01:01,name,class
I used How to add new column with header to csv with awk
for reference.
ORIG_FILE='sample.csv'
NEW_FILE='new_sample.csv'
values="01-01-2020 01:01:01,name,class"
awk -v d=$values -F"," 'BEGIN {OFS = ","} {printf("%s%s",$0,FNR>1?d RS:"col4,col5,col6" RS)}' $ORIG_FILE > $NEW_FILE
I am very new to using bash and I am trying to figure this out.
Any help greatly appreciated.


orig_file='sample.csv'
new_file='new_sample.csv'
values='01-01-2020 01:01:01,name,class'
awk -v d="$values" 'BEGIN{FS=OFS=","} { print $0, (NR>1 ? d : "col4,col5,col6") }' "$orig_file" > "$new_file"
Always quote your shell variables and don't use all upper case for non-exported shell variable names.

Related

Can I delete a field in awk?

This is test.txt:
0x01,0xDF,0x93,0x65,0xF8
0x01,0xB0,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,0xB2,0x00,0x76
If I run
awk -F, 'BEGIN{OFS=","}{$2="";print $0}' test.txt
the result is:
0x01,,0x93,0x65,0xF8
0x01,,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,,0x00,0x76
The $2 wasn't deleted, it just became empty.
I hope, when printing $0, that the result is:
0x01,0x93,0x65,0xF8
0x01,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,0x00,0x76

All the existing solutions are good though this is actually a tailor made job for cut:
cut -d, -f 1,3- file
0x01,0x93,0x65,0xF8
0x01,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,0x00,0x76
If you want to remove 3rd field then use:
cut -d, -f 1,2,4- file
To remove 4th field use:
cut -d, -f 1-3,5- file

I believe simplest would be to use sub function to replace first occurrence of continuous ,,(which are getting created after you made 2nd field NULL) with single ,. But this assumes that you don't have any commas in between field values.
awk 'BEGIN{FS=OFS=","}{$2="";sub(/,,/,",");print $0}' Input_file
2nd solution: OR you could use match function to catch regex from first comma to next comma's occurrence and get before and after line of matched string.
awk '
match($0,/,[^,]*,/){
print substr($0,1,RSTART-1)","substr($0,RSTART+RLENGTH)
}' Input_file

It's a bit heavy-handed, but this moves each field after field 2 down a place, and then changes NF so the unwanted field is not present:
$ awk -F, -v OFS=, '{ for (i = 2; i < NF; i++) $i = $(i+1); NF--; print }' test.txt
0x01,0x93,0x65,0xF8
0x01,0x01,0x03,0x02,0x00,0x64,0x06,0x01
0x01,0x00,0x76
$
Tested with both GNU Awk 4.1.3 and BSD Awk ("awk version 20070501" on macOS Mojave 10.14.6 — don't ask; it frustrates me too, but sometimes employers are not very good at forward thinking). Setting NF may or may not work on older versions of Awk — I was a little surprised it did work, but the surprise was a pleasant one, for a change.

If Awk is not an absolute requirement, and the input is indeed as trivial as in your example, sed might be a simpler solution.
sed 's/,[^,]*//' test.txt
This is especially elegant if you want to remove the second field. A more generic approach to remove, the nth field would require you to put in a regex which matches the first n - 1 followed by the nth, then replace that with just the the first n - 1.
So for n = 4 you'd have
sed 's/\([^,]*,[^,]*,[^,]*,\)[^,]*,/\1/' test.txt
or more generally, if your sed dialect understands braces for specifying repetitions
sed 's/\(\([^,]*,\)\{3\}\)[^,]*,/\1/' test.txt
Some sed dialects allow you to lose all those pesky backslashes with an option like -r or -E but again, this is not universally supported or portable.
In case it's not obvious, [^,] matches a single character which is not (newline or) comma; and \1 recalls the text from first parenthesized match (back reference; \2 recalls the second, etc).
Also, this is completely unsuitable for escaped or quoted fields (though I'm not saying it can't be done). Every comma acts as a field separator, no matter what.

With GNU sed you can add a number modifier to substitute nth match of non-comma characters followed by comma:
sed -E 's/[^,]*,//2' file

Using awk in a regex-free way, with the option to choose which line will be deleted:
awk '{ col = 2; n = split($0,arr,","); line = ""; for (i = 1; i <= n; i++) line = line ( i == col ? "" : ( line == "" ? "" : "," ) arr[i] ); print line }' test.txt
Step by step:
{
col = 2 # defines which column will be deleted
n = split($0,arr,",") # each line is split into an array
# n is the number of elements in the array
line = "" # this will be the new line
for (i = 1; i <= n; i++) # roaming through all elements in the array
line = line ( i == col ? "" : ( line == "" ? "" : "," ) arr[i] )
# appends a comma (except if line is still empty)
# and the current array element to the line (except when on the selected column)
print line # prints line
}

Another solution:
You can just pipe the output to another sed and squeeze the delimiters.
$ awk -F, 'BEGIN{OFS=","}{$2=""}1 ' edward.txt | sed 's/,,/,/g'
0x01,0x93,0x65,0xF8
0x01,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,0x00,0x76
$

Commenting on the first solution of #RavinderSingh13 using sub() function:
awk 'BEGIN{FS=OFS=","}{$2="";sub(/,,/,",");print $0}' Input_file
The gnu-awk manual: https://www.gnu.org/software/gawk/manual/html_node/Changing-Fields.html
It is important to note that making an assignment to an existing field changes the value of $0 but does not change the value of NF, even when you assign the empty string to a field." (4.4 Changing the Contents of a Field)
So, following the first solution of RavinderSingh13 but without using, in this case,sub() "The field is still there; it just has an empty value, delimited by the two colons":
awk 'BEGIN {FS=OFS=","} {$2="";print $0}' file
0x01,,0x93,0x65,0xF8
0x01,,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,,0x00,0x76

My solution:
awk -F, '
{
regex = "^"$1","$2
sub(regex, $1, $0);
print $0;
}'
or one line code:
awk -F, '{regex="^"$1","$2;sub(regex, $1, $0);print $0;}' test.txt
I found that OFS="," was not necessary

I would do it following way, let file.txt content be:
0x01,0xDF,0x93,0x65,0xF8
0x01,0xB0,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,0xB2,0x00,0x76
then
awk 'BEGIN{FS=",";OFS=""}{for(i=2;i<=NF;i+=1){$i="," $i};$2="";print}' file.txt
output
0x01,0x93,0x65,0xF8
0x01,0x01,0x03,0x02,0x00,0x64,0x06,0x01,0xB0
0x01,0x00,0x76
Explanation: I set OFS to nothing (empty string), then for 2nd and following column I add , at start. Finally I set what is now comma and value to nothing. Keep in mind this solution would need rework if you wish to remove 1st column.

How to print all columns in filtered condition for column using awk?

I have comma separated file and i need to filter the file based upon some columns values; i am using following command which is giving me required result but i am unable to print all columns using following command.
The following command is giving me all columns avoiding filter; so the target file is same as size as source.
This is the command i am using
awk 'BEGIN{ FS=OFS=","}{ if($7=="\"3YM62AE#UUS\"" && $5=="\"01CS\""){ print $0 }}' file1.csv > file2.csv

in your awk script ignore double quotes. Try something like:
awk 'BEGIN { FS=OFS=","} $7=="3YM62AE#UUS" && $5=="01CS" { print }' file1.csv > file2.csv

Split rows to multiple line based on comma : one liner solution

I want to split the following format to unique lines
Input:
17:79412041:C:T,CGGATGTCAT
17:79412059:C:G,T
17:79412138:G:A,C
17:79412192:C:G,T,A
Desired output
17:79412041:C:T
17:79412041:C:CGGATGTCAT
17:79412059:C:G
17:79412059:C:T
17:79412138:G:A
17:79412138:G:C
17:79412192:C:G
17:79412192:C:T
17:79412192:C:A
Basically split the input to unique rows or firstID:secondID:thirdID:FourthID. Here multiple row may have firstID:secondID:thirdID may be common and the FourthID is the one it make each raw unique(that was seperated by "," in the input).
Thanks in advance
Shams

awk one-liner
$ awk -F":" '{gsub(/,/,":"); a=$1FS$2FS$3; for(i=4; i<=NF; i++) print a FS $i;}' f1
17:79412041:C:T
17:79412041:C:CGGATGTCAT
17:79412059:C:G
17:79412059:C:T
17:79412138:G:A
17:79412138:G:C
17:79412192:C:G
17:79412192:C:T
17:79412192:C:A
We are first replacing all , with : to keep a common delimiter i.e. :
We are then traversing from 4th field to end and printing each field by prefixing first three fields.

This one-liner here:
$ awk -F':' '{ split($4,a,","); for (i in a) { print $1":"$2":"$3":"a[i] } }' data.txt
Produces:
17:79412041:C:T
17:79412041:C:CGGATGTCAT
17:79412059:C:G
17:79412059:C:T
17:79412138:G:A
17:79412138:G:C
17:79412192:C:G
17:79412192:C:T
17:79412192:C:A
Explanation:
split(string, array, delimiter)
splits the string by the delimiter, and saves the pieces into the array.
The for-in loop simply prints every piece in the array with the first three entries.
The -F':' part defines the top-level delimiter.

another awk, should work for any number of fields
$ awk -F: '{split($NF,a,","); for(i in a) {sub($NF"$",a[i]); print}}' file

Following awk + gsub of it may help you on same too:
awk -F":" '{gsub(",",ORS $1 OFS $2 OFS $3 "&");gsub(/,/,":")} 1' OFS=":" Input_file

This might work for you (GNU sed):
sed 's/^\(\(.*:\)[^:,]*\),/\1\n\2/;P;D' file
Insert a newline and the key for each comma in a line.
An alternative using a loop and syntactic sugar:
sed -r ':a;s/^((.*:)[^:,]*),/\1\n\2/;ta' file

How do I set set values in multiple fields using awk?

Say I have the following data in a file (file.txt):
one|two|three|four|five|six
And I want to prefix field one ($1) with an "A" and I want to prefix field three ($3) with a "B". What would my awk script look like? I tried:
awk -F "|" -OFS='|' '
{
$1 = "A"$1
$3 = "B"$3
print;
}
' file.txt
But this didn't work. The output was:
Aone|two|three|four|five|six B
Sorry, I'm not great awk programmer here.

Looks like I figured it out. It had to do with the output field separator (OFS). If I issue the following it works:
awk -F "|" 'BEGIN{OFS="|";}{$1="A"$1;$3="B"$3; print}' file.txt
The OFS value has to be inside the script and not passed as an parameter to awk. Not exactly sure why.

Using the flag -OFS='|' is setting the field separator to S=|. Just do
awk '...' FS=\| OFS=\| file.txt

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