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Or Ravinder's solution slightly changed
awk 'FNR==NR{A[$1];next} ($1 in A){print $1,$2} ($2 in A){print $2,$1}' file1 file2
The order of the output is the one of file2.

Try awk '
FNR==NR {C[$1]++
R[$1,C[$1]]=$2
C[$2]++
R[$2,C[$2]]=$1
next
}
$1 in C {for (i=1;...

Hello Syeda,

Could you please try following and let me know if this helps you.

awk '{A=$1}($1 != $2){A=$1 OFS $2} ($1 != $3){A=A?A OFS $3:$3} {print A;A=""}' Input_file
Output will be as...

Hello Syeda,

Could you please try following and let me know if this helps.

awk '{for(i=2;i<=NF;i++){sub(/\;/,X,$i);print $1 OFS $i}}' Input_file
Output will be as follows.

P38112 Q12389...

With grep:
grep -v 'refseq:NP.*refseq:NP' file
Not asked here, but I want to mention that sed can delete the nth occurrence, here the 2nd:
sed 's/|refseq:NP[_0-9]*//2' file

---------- Post...

Try alsoawk '2==gsub(/refseq:NP/,"&")' file
DIP-23436N|refseq:NP_536784 DIP-23130N|refseq:NP_652017
DIP-22958N|refseq:NP_651195 DIP-20072N|refseq:NP_724597
DIP-22928N|refseq:NP_569972 ...

Hello Syeda,

Could you please try following and let me know if this helps.

awk '{count=gsub(/refseq:NP/,"refseq:NP",$0);if(count==NF){print}}' Input_file
Output will be as follows.
...

Perhaps something more like:
awk '
BEGIN { printf(" ")
s = "sort"
}
FNR == 1 {
printf(" %s", files[++fc] = FILENAME)
}
{ d[$1, fc] = $2
c1[$1]
}
END { print ""
for(i in c1) {...

Hello Syeda,

For file1 and file2, could you please try following and let me know if this helps.

awk 'BEGIN{print " file1 file2"}FNR==NR{;A[$1]=$NF;next} ($1 in A){print $1 OFS A[$1] OFS...

Hello Syeda,

Not sure which command you have used, following and post#2 command provided be me works fine for me as follows.

awk 'BEGIN{print " file1 file2"}FNR==NR{;A[$1]=$NF;next} ($1 in...

Different approach:awk '/^ *C/ {if (L) print NR-L-1; printf "%s\t", $2; L=NR} END {print NR-L}' file
0001 5
0002 0
0003 0
0004 2
0005 2

The second solution more "verbose":
awk '
function pr() {if (notfirst++) print heading,dcnt}
$1=="C" {pr(); heading=$2; dcnt=0}
$1=="D" {dcnt++}
END {pr()}
' file

Hi, try:
awk '$1=="C"{i=$2; A[i]=0} $1=="D"{A[i]++} END{for(i in A) print i,A[i]}' file

or

awk '$1=="C"{if(i!="") print i, c; i=$2; c=0} $1=="D"{c++} END{print i, c}' file

Hello Syeda,

Here is an example suppose you want to substitute the 2nd occurrence of _ in $2 then following may help you.
Input_file:

Ravinder gi_49482297_ref_YP_039521.1_ TESTing test123...

Hello Syeda,

If you want to only substitute $2's _ present at last of $2then following may help you. As you had mentioned in first post that you need to substitute other columns _ too so I have...

Hello Syeda,

Following may help you in same, let's say you have a Input_file as follows(which is an example as you haven't shown us complete input and didn't tell us about field separator so I am...