skip if match all but n columns of previous line - awk
I have a large csv file with consecutive repeated rows except for the time related columns (columns 1, 2, 3, 4) I want to skip except for the first occurence (non-consecutive repeated rows are ok).
Is there a more efficient way than the below code? (I also don't want to painfully hard code that condition, say when I have more than 9 columns)
awk -F"," -v OFS="," 'p[5]!=$5 || p[6]!=$6 || p[7]!=$7 || p[8]!=$8 || p[9]!=$9 {for (i = 5; i <= 9; i++) {p[i] = $i}; print $0}' file_path
Example input:
a,z,k,d,5,6,7,8,9
b,x,j,d,5,6,7,8,9
c,c,l,e,8,9,1,2,3
d,v,k,r,8,9,1,2,3
e,b,j,e,9,1,2,3,4
f,n,h,t,5,6,7,8,9
g,m,g,w,6,3,4,5,6
h,a,f,q,4,5,6,7,8
i,s,d,w,4,5,6,7,8
i,s,d,w,4,5,6,7,8
Desired output:
a,z,k,d,5,6,7,8,9
c,c,l,e,8,9,1,2,3
e,b,j,e,9,1,2,3,4
f,n,h,t,5,6,7,8,9
g,m,g,w,6,3,4,5,6
h,a,f,q,4,5,6,7,8
Is this what you're trying to do?
$ awk '{prev=key; key=$0; sub(/([^,]*,){4}/,"",key)} key != prev' file
a,z,k,d,5,6,7,8,9
c,c,l,e,8,9,1,2,3
e,b,j,e,9,1,2,3,4
f,n,h,t,5,6,7,8,9
g,m,g,w,6,3,4,5,6
h,a,f,q,4,5,6,7,8
if you don't have space if the fields
$ sed 's/,/ /4' file | uniq -f1 | sed 's/ /,/'
since uniq doesn't work with arbitrary delimiters.
One awk idea:
awk '
BEGIN { regex="([^,]+,){4}" } # match first 4x "column," sets
{ match($0,regex)
curr=substr($0,RSTART+RLENGTH) # strip off first 4x "column," sets
if (curr == prev) next # if the same as previous row then go to next input
else { print; prev=curr } # else print current line and set prev = current line
}
' file
This generates:
a,z,k,d,5,6,7,8,9
c,c,l,e,8,9,1,2,3
e,b,j,e,9,1,2,3,4
f,n,h,t,5,6,7,8,9
g,m,g,w,6,3,4,5,6
h,a,f,q,4,5,6,7,8
Using GNU sed
$ sed -En 'G;/^([^,]*,){4}([^\n]*)\n([^,]*,){4}\2/d;h;P' input_file
a,z,k,d,5,6,7,8,9
c,c,l,e,8,9,1,2,3
e,b,j,e,9,1,2,3,4
f,n,h,t,5,6,7,8,9
g,m,g,w,6,3,4,5,6
h,a,f,q,4,5,6,7,8
Related
Keep current and previous line only if current line fulfills a given condition
I have a file which looks like this: >4RYF_1 MAENTKNENITNILTQKLIDTRTVLIYGEINQELAEDVSKQLLLLESISNDPITIFINSQGGHVEAGDTIHDMIKFIKPTVKVVGTGWVASAGITIYLAAEKENRFSLPNTRYMIHQPAGGVQGQSTEIEIEAKEIIRMRERINRLIAEATGQSYEQISKDTDRNFWLSVNEAKDYGIVNEIIENRDGLKMASWSHPQFEK >4RYF_2 MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH I want to keep the sequence and previous line only if the sequence has a given length. For selecting only lines with that condition I use: awk 'length($0) > 50 && length($0) <=800)' sample.txt But how can I keep lines starting with > as well if this condition is met?
Yet another awk solution:
awk '/^>/ { header = $0; next } length > 50 && length <= 800 { print header ORS $0 }'
Would you please try the following:
awk -v RS='>' -F'\n' '
length($2) > 50 && length($2) <= 800 {printf ">%s", $0}
' sample.txt
Assigning RS to '>' tells awk to split the file on > into records,
treating the header line and the sequence line in the same record.
Assigning FS to '\n' splits the record to the header and
sequence, each assigning $1 to the header and $2 to the sequence.
As the leading > is chopped off as a delimiter, we need to prepend it
when printing the matched records.
Here is one-liner:
LANG=C grep -B1 '^.\{51,800\}$' < sample.txt
The command was really slow with LANG=en_US.UTF-8 that I set by default, so using LANG=C instead.
man grep tells you that '-B NUM' means ' Print NUM lines of leading context before matching lines.'.
'^' means start of line
'.' means any character
'{51,800}' means we want between 51 and 800 of the previous thing
'$' means end of line.
Or in other words, we want to match lines that are between 51 and 800 characters, and print it and the previous line.
A potential solution with AWK is:
awk '!/^>/ {next}; {getline s}; length(s) > 50 && length(s) <= 800 { print $0 "\n" s }' example.fasta
e.g. if example.fasta contains
>4RYF_1
WLSVNEAKDYGIVNEIIENRDGLKMASWSHPQFEK
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH
>1000_chars
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
It will only print
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH
Edit
The method that I would recommend to better handle edge-cases is to use purpose-built bioinformatics software, e.g. seqkit
seqkit seq -m 50 -M 800 example.fasta
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDI
FLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEI
MIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEA
KDYGLIDDIIINKSGLKGHHHHHH
Is perl an option?
perl -nle '$prev && print if length() >50 and length() < 800 && print $prev; $prev = $_' input_file
$prev - Create a variable which will hold every line. When the length condition is met, and there has been a previous line $prev, then it prints the condition matched in $prev and prints the last line.
$prev = $_ Assigns the current line to the prev line variable
If the upper limit 800 is not essential, could sed be an option?
$ sed -En '/>/ {N;/[a-zA-Z0-9]{50,}/p}' input_file
/>/ - Match > and read into the pattern space
N; Run the condition on the next line after the match and append that to the pattern space also:
{50,} - If the length is 50 or more
\1/p - Return it and print
Output
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH
With your shown samples, please try following awk code. Written and tested with GNU awk.
awk -v RS= '
{
val=""
delete arr
while(match($0,/>[^\n]*\n*[^\n]*/)){
val=substr($0,RSTART,RLENGTH)
split(val,arr,"\n")
if(length(arr[2])>50 && length(arr[2])<=800){
print val
}
$0=substr($0,RSTART+RLENGTH)
}
}
' Input_file
If only the next line should meet the length restrictions, you can match and store the line that starts with > in a variable, for example previous
Then for the next line, check for the length and if the previous line is not empty.
If is is not, print the previous and the current line.
At the end, set the previous variable to an empty string.
awk '{
if (/^>/) {
previous = $0
next
}
if (length(previous) != 0 && length($0) > 50 && length($0) <= 800) {
print previous ORS $0
}
previous=""
}' sample.txt
See an AWK demo
linux csv file concatenate columns into one column
I've been looking to do this with sed, awk, or cut. I am willing to use any other command-line program that I can pipe data through.
I have a large set of data that is comma delimited. The rows have between 14 and 20 columns. I need to recursively concatenate column 10 with column 11 per row such that every row has exactly 14 columns. In other words, this:
a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p
will become:
a,b,c,d,e,f,g,h,i,jkl,m,n,o,p
I can get the first 10 columns. I can get the last N columns. I can concatenate columns. I cannot think of how to do it in one line so I can pass a stream of endless data through it and end up with exactly 14 columns per row.
Examples (by request):
How many columns are in the row?
sed 's/[^,]//g' | wc -c
Get the first 10 columns:
cut -d, -f1-10
Get the last 4 columns:
rev | cut -d, -f1-4 | rev
Concatenate columns 10 and 11, showing columns 1-10 after that:
awk -F',' ' NF { print $1","$2","$3","$4","$5","$6","$7","$8","$9","$10$11}'
Awk solution:
awk 'BEGIN{ FS=OFS="," }
{
diff = NF - 14;
for (i=1; i <= NF; i++)
printf "%s%s", $i, (diff > 1 && i >= 10 && i < (10+diff)?
"": (i == NF? ORS : ","))
}' file
The output:
a,b,c,d,e,f,g,h,i,jkl,m,n,o,p
With GNU awk for the 3rd arg to match() and gensub():
$ cat tst.awk
BEGIN{ FS="," }
match($0,"(([^,]+,){9})(([^,]+,){"NF-14"})(.*)",a) {
$0 = a[1] gensub(/,/,"","g",a[3]) a[5]
}
{ print }
$ awk -f tst.awk file
a,b,c,d,e,f,g,h,i,jkl,m,n,o,p
If perl is okay - can be used just like awk for stream processing
$ cat ip.txt
a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p
1,2,3,4,5,6,3,4,2,4,3,4,3,2,5,2,3,4
1,2,3,4,5,6,3,4,2,4,a,s,f,e,3,4,3,2,5,2,3,4
$ awk -F, '{print NF}' ip.txt
16
18
22
$ perl -F, -lane '$n = $#F - 4;
print join ",", (#F[0..8], join("", #F[9..$n]), #F[$n+1..$#F])
' ip.txt
a,b,c,d,e,f,g,h,i,jkl,m,n,o,p
1,2,3,4,5,6,3,4,2,43432,5,2,3,4
1,2,3,4,5,6,3,4,2,4asfe3432,5,2,3,4
-F, -lane split on , results saved in #F array
$n = $#F - 4 magic number, to ensure output ends with 14 columns. $#F gives the index of last element of array (won't work if input line has less than 14 columns)
join helps to stitch array elements together with specified string
#F[0..8] array slice with first 9 elements
#F[9..$n] and #F[$n+1..$#F] the other slices as needed
Borrowing from Ed Morton's regex based solution
$ perl -F, -lape '$n=$#F-13; s/^([^,]*,){9}\K([^,]*,){$n}/$&=~tr|,||dr/e' ip.txt
a,b,c,d,e,f,g,h,i,jkl,m,n,o,p
1,2,3,4,5,6,3,4,2,43432,5,2,3,4
1,2,3,4,5,6,3,4,2,4asfe3432,5,2,3,4
$n=$#F-13 magic number
^([^,]*,){9}\K first 9 fields
([^,]*,){$n} fields to change
$&=~tr|,||dr use tr to delete the commas
e this modifier allows use of Perl code in replacement section
this solution also has the added advantage of working even if input field is less than 14
You can try this gnu sed
sed -E '
s/,/\n/9g
:A
s/([^\n]*\n)(.*)(\n)(([^\n]*\n){4})/\1\2\4/
tA
s/\n/,/g
' infile
First variant - with awk
awk -F, '
{
for(i = 1; i <= NF; i++) {
OFS = (i > 9 && i < NF - 4) ? "" : ","
if(i == NF) OFS = "\n"
printf "%s%s", $i, OFS
}
}' input.txt
Second variant - with sed
sed -r 's/,/#/10g; :l; s/#(.*)((#[^#]){4})/\1\2/; tl; s/#/,/g' input.txt
or, more straightforwardly (without loop) and probably faster.
sed -r 's/,(.),(.),(.),(.)$/#\1#\2#\3#\4/; s/,//10g; s/#/,/g' input.txt
Testing
Input
a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p
a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r
a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u
Output
a,b,c,d,e,f,g,h,i,jkl,m,n,o,p
a,b,c,d,e,f,g,h,i,jklmn,o,p,q,r
a,b,c,d,e,f,g,h,i,jklmnopq,r,s,t,u
Solved a similar problem using csvtool. Source file, copied from one of the other answers: $ cat input.txt a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p 1,2,3,4,5,6,3,4,2,4,3,4,3,2,5,2,3,4 1,2,3,4,5,6,3,4,2,4,a,s,f,e,3,4,3,2,5,2,3,4 Concatenating columns: $ cat input.txt | csvtool format '%1,%2,%3,%4,%5,%6,%7,%8,%9,%10%11%12,%13,%14,%15,%16,%17,%18,%19,%20,%21,%22\n' - a,b,c,d,e,f,g,h,i,jkl,m,n,o,p,,,,,, 1,2,3,4,5,6,3,4,2,434,3,2,5,2,3,4,,,, 1,2,3,4,5,6,3,4,2,4as,f,e,3,4,3,2,5,2,3,4 anatoly#anatoly-workstation:cbs$ cat input.txt
How to use awk sort by column 3
I have a file (user.csv)like this
ip,hostname,user,group,encryption,aduser,adattr
want to print all column sort by user,
I tried awk -F ":" '{print|"$3 sort -n"}' user.csv , it doesn't work.
How about just sort. sort -t, -nk3 user.csv where -t, - defines your delimiter as ,. -n - gives you numerical sort. Added since you added it in your attempt. If your user field is text only then you dont need it. -k3 - defines the field (key). user is the third field.
Use awk to put the user ID in front.
Sort
Use sed to remove the duplicate user ID, assuming user IDs do not contain any spaces.
awk -F, '{ print $3, $0 }' user.csv | sort | sed 's/^.* //'
Seeing as that the original question was on how to use awk and every single one of the first 7 answers use sort instead, and that this is the top hit on Google, here is how to use awk.
Sample net.csv file with headers:
ip,hostname,user,group,encryption,aduser,adattr
192.168.0.1,gw,router,router,-,-,-
192.168.0.2,server,admin,admin,-,-,-
192.168.0.3,ws-03,user,user,-,-,-
192.168.0.4,ws-04,user,user,-,-,-
And sort.awk:
#!/usr/bin/awk -f
# usage: ./sort.awk -v f=FIELD FILE
BEGIN {
FS=","
}
# each line
{
a[NR]=$0 ""
s[NR]=$f ""
}
END {
isort(s,a,NR);
for(i=1; i<=NR; i++) print a[i]
}
#insertion sort of A[1..n]
function isort(S, A, n, i, j) {
for( i=2; i<=n; i++) {
hs = S[j=i]
ha = A[j=i]
while (S[j-1] > hs) {
j--;
S[j+1] = S[j]
A[j+1] = A[j]
}
S[j] = hs
A[j] = ha
}
}
To use it:
awk sort.awk f=3 < net.csv # OR
chmod +x sort.awk
./sort.awk f=3 net.csv
You can choose a delimiter, in this case I chose a colon and printed the column number one, sorting by alphabetical order:
awk -F\: '{print $1|"sort -u"}' /etc/passwd
awk -F, '{ print $3, $0 }' user.csv | sort -nk2
and for reverse order
awk -F, '{ print $3, $0 }' user.csv | sort -nrk2
try this -
awk '{print $0|"sort -t',' -nk3 "}' user.csv
OR
sort -t',' -nk3 user.csv
awk -F "," '{print $0}' user.csv | sort -nk3 -t ','
This should work
To exclude the first line (header) from sorting, I split it out into two buffers.
df | awk 'BEGIN{header=""; $body=""} { if(NR==1){header=$0}else{body=body"\n"$0}} END{print header; print body|"sort -nk3"}'
With GNU awk:
awk -F ',' '{ a[$3]=$0 } END{ PROCINFO["sorted_in"]="#ind_str_asc"; for(i in a) print a[i] }' file
See 8.1.6 Using Predefined Array Scanning Orders with gawk for more sorting algorithms.
I'm running Linux (Ubuntu) with mawk:
tmp$ awk -W version
mawk 1.3.4 20200120
Copyright 2008-2019,2020, Thomas E. Dickey
Copyright 1991-1996,2014, Michael D. Brennan
random-funcs: srandom/random
regex-funcs: internal
compiled limits:
sprintf buffer 8192
maximum-integer 2147483647
mawk (and gawk) has an option to redirect the output of print to a command. From man awk chapter 9. Input and output:
The output of print and printf can be redirected to a file or command by appending > file, >> file or | command to the end of the print statement. Redirection opens file or command only once, subsequent redirections append to the already open stream.
Below you'll find a simplied example how | can be used to pass the wanted records to an external program that makes the hard work. This also nicely encapsulates everything in a single awk file and reduces the command line clutter:
tmp$ cat input.csv
alpha,num
D,4
B,2
A,1
E,5
F,10
C,3
tmp$ cat sort.awk
# print header line
/^alpha,num/ {
print
}
# all other lines are data lines that should be sorted
!/^alpha,num/ {
print | "sort --field-separator=, --key=2 --numeric-sort"
}
tmp$ awk -f sort.awk input.csv
alpha,num
A,1
B,2
C,3
D,4
E,5
F,10
See man sort for the details of the sort options:
-t, --field-separator=SEP
use SEP instead of non-blank to blank transition
-k, --key=KEYDEF
sort via a key; KEYDEF gives location and type
-n, --numeric-sort
compare according to string numerical value
Using awk to pull specific lines from a file
I have two files, one file is my data, and the other file is a list of line numbers that I want to extract from my data file. Can I use awk to read in my lines file, and then extract the lines that match the line numbers? Example: Data file: This is the first line of my data This is the second line of my data This is the third line of my data This is the fourth line of my data This is the fifth line of my data Line numbers file 1 4 5 Output: This is the first line of my data This is the fourth line of my data This is the fifth line of my data I've only ever used command line awk and sed for really simple stuff. This is way beyond me and I have been googling for an hour without an answer.
awk 'NR == FNR {nums[$1]; next} FNR in nums' numberfile datafile
simply referring to an array subscript creates the entry. Looping over the first file, while NR (record number) is equal to FNR (file record number) using the next statement stores all the line numbers in the array. After that when FNR of the second file is present in the array (true) the line is printed (which is the default action for "true").
One way with sed:
sed 's/$/p/' linesfile | sed -n -f - datafile
You can use the same trick with awk:
sed 's/^/NR==/' linesfile | awk -f - datafile
Edit - Huge files alternative
With regards to huge number of lines it is not prudent to keep whole files in memory. The solution in that case can be to sort the numbers-file and read one line at a time. The following has been tested with GNU awk:
extract.awk
BEGIN {
getline n < linesfile
if(length(ERRNO)) {
print "Unable to open linesfile '" linesfile "': " ERRNO > "/dev/stderr"
exit
}
}
NR == n {
print
if(!(getline n < linesfile)) {
if(length(ERRNO))
print "Unable to open linesfile '" linesfile "': " ERRNO > "/dev/stderr"
exit
}
}
Run it like this:
awk -v linesfile=$linesfile -f extract.awk infile
Testing:
echo "2
4
7
8
10
13" | awk -v linesfile=/dev/stdin -f extract.awk <(paste <(seq 50e3) <(seq 50e3 | tac))
Output:
2 49999
4 49997
7 49994
8 49993
10 49991
13 49988
Here is an awk example. inputfile is loaded up front, then matching records of datafile are output.
awk \
-v RS="[\r]*[\n]" \
-v FILE="inputfile" \
'BEGIN \
{
LINES = ","
while ((getline Line < FILE))
{
LINES = LINES Line ","
}
}
LINES ~ "," NR "," \
{
print
}
' datafile
I had the same problem. This is the solution already posted by Thor:
cat datafile \
| awk 'BEGIN{getline n<"numbers"} n==NR{print; getline n<"numbers"}'
If like me you don't have a numbers file, but it is instead passed on from stdin and you don't want to generate a temporary numbers file, then this is an alternative solution:
cat numbers \
| awk '{while((getline line<"datafile")>0) {n++; if(n==$0) {print line;next}}}'
This solution...
awk 'NR == FNR {nums[$1]; next} FNR in nums' numberfile datafile
...only prints unique numbers in the numberfile. What if the numberfile contains repeated entries? Then sed is a better (but much slower) alternative:
sed -nf <(sed 's/.*/&p/' numberfile) datafile
while read line; do echo $(sed -n '$(echo $line)p' Datafile.txt); done < numbersfile.txt
Is there a way to completely delete fields in awk, so that extra delimiters do not print?
Consider the following command:
$ gawk -F"\t" "BEGIN{OFS=\"\t\"}{$2=$3=\"\"; print $0}" Input.tsv
When I set $2 = $3 = "", the intended effect is to get the same effect as writing:
print $1,$4,$5...$NF
However, what actually happens is that I get two empty fields, with the extra field delimiters still printing.
Is it possible to actually delete $2 and $3?
Note: If this was on Linux in bash, the correct statement above would be the following, but Windows does not handle single quotes well in cmd.exe.
$ gawk -F'\t' 'BEGIN{OFS="\t"}{$2=$3=""; print $0}' Input.tsv
This is an oldie but goodie.
As Jonathan points out, you can't delete fields in the middle, but you can replace their contents with the contents of other fields. And you can make a reusable function to handle the deletion for you.
$ cat test.awk
function rmcol(col, i) {
for (i=col; i<NF; i++) {
$i = $(i+1)
}
NF--
}
{
rmcol(3)
}
1
$ printf 'one two three four\ntest red green blue\n' | awk -f test.awk
one two four
test red blue
You can't delete fields in the middle, but you can delete fields at the end, by decrementing NF.
So you can shift all the later fields down to overwrite $2 and $3 then decrement NF by two, which erases the last two fields:
$ echo 1 2 3 4 5 6 7 | awk '{for(i=2; i<NF-1; ++i) $i=$(i+2); NF-=2; print $0}'
1 4 5 6 7
If you are just looking to remove columns, you can use cut:
$ cut -f 1,4- file.txt
To emulate cut:
$ awk -F "\t" '{ for (i=1; i<=NF; i++) if (i != 2 && i != 3) { if (i == NF) printf $i"\n"; else printf $i"\t" } }' file.txt
Similarly:
$ awk -F "\t" '{ delim =""; for (i=1; i<=NF; i++) if (i != 2 && i != 3) { printf delim $i; delim = "\t"; } printf "\n" }' file.txt
HTH
The only way I can think to do it in Awk without using a loop is to use gsub on $0 to combine adjacent FS:
$ echo {1..10} | awk '{$2=$3=""; gsub(FS"+",FS); print}'
1 4 5 6 7 8 9 10
One way could be to remove fields like you do and remove extra spaces with gsub:
$ awk 'BEGIN { FS = "\t" } { $2 = $3 = ""; gsub( /\s+/, "\t" ); print }' input-file
In the addition of the answer by Suicidal Steve I'd like to suggest one more solution but using sed instead awk. It seems more complicated than usage of cut as it was suggested by Steve. But it was the better solution because sed -i allows editing in-place. $ sed -i 's/\(.*,\).*,.*,\(.*\)/\1\2/' FILENAME
To remove fields 2 and 3 from a given input file (assuming a tab field separator), you can remove the fields from $0 using gensub and regenerate it as follows:
awk -F '\t' 'BEGIN{OFS="\t"}\
{$0=gensub(/[^\t]*\t/,"",3);\
$0=gensub(/[^\t]*\t/,"",2);\
print}' Input.tsv
The method presented in the answer of ghoti has some problems:
every assignment of $i = $(i+1) forces awk to rebuild the record $0. This implies that if you have 100 fields and you want to delete field 10, you rebuild the record 90 times.
changing the value of NF manually is not posix compliant and leads to undefined behaviour (as is mentioned in the comments).
A somewhat more cumbersome, but stable robust way to delete a set of columns would be:
a single column:
awk -v del=3 '
BEGIN{FS=fs;OFS=ofs}
{ b=""; for(i=1;i<=NF;++i) if(i!=del) b=(b?b OFS:"") $i; $0=b }
# do whatever you want to do
' file
multiple columns:
awk -v del=3,5,7 '
BEGIN{FS=fs;OFS=ofs; del="," del ","}
{ b=""; for(i=1;i<=NF;++i) if (del !~ ","i",") b=(b?b OFS:"") $i; $0=b }
# do whatever you want to do
' file
Well, if the goal is to remove the extra delimiters, then you can use tr on Linux. Example: $ echo "1,2,,,5" | tr -s ',' 1,2,5
echo one two three four five six|awk '{
print $0
is3=$3
$3=""
print $0
print is3
}'
one two three four five six
one two four five six
three