awk to update specific value in file with match and add +1 to specific digit

Shell Programming and Scripting
1

I am trying to use awk to match the NM_ in file with $1 of id which is tab-delimited . The NM_ will always be in the line of file that starts with > and be after the second _ . When there is a match between each NM_ and id , then the value of $2 in id is substituted or used to update the NM_ . Each NM_ may not be unique, as in the example below, but will have a match in id .

After the third _ there is a digit 0,1,2,etc that I am trying to add the word exon and add +1 to the digit. Not sure if my awk attempt helps at all to address the first question. Thank you :).

file

>hg19_refGene_NM_001195684_0 range=chr1:92327018-92327098 5'pad=10 3'pad=10 strand=- repeatMasking=none
agaaataaaaATGACTTCCCATTATGTGATTGCCATCTTTGCCCTGATGA
GCTCCTGTTTAGCCACTGCAGgtaagttgca
>hg19_refGene_NM_001195684_1 range=chr1:92262834-92263038 5'pad=10 3'pad=10 strand=- repeatMasking=none
cccttggcagGTCCAGAGCCTGGTGCACTGTGTGAACTGTCACCTGTCAG
TGCCTCCCATCCTGTCCAGGCCTTGATGGAGAGCTTCACTGTTTTGTCAG
GCTGTGCCAGCAGAGGCACAACTGGGCTGCCACAGGAGGTGCATGTCCTG
AATCTCCGCACTGCAGGCCAGGGGCCTGGCCAGCTACAGAGAGAGgtagg
tgcag
>hg19_refGene_NM_001195684_2 range=chr1:92224160-92224317 5'pad=10 3'pad=10 strand=- repeatMasking=none
tgcttcctagGTCACACTTCACCTGAATCCCATCTCCTCAGTCCACATCC
ACCACAAGTCTGTTGTGTTCCTGCTCAACTCCCCACACCCCCTGGTGTGG
CATCTGAAGACAGAGAGACTTGCCACTGGGGTCTCCAGACTGTTTTTGgt
aagtgctt
>hg19_refGene_NM_001195683_2 range=chr1:92224160-92224317 5'pad=10 3'pad=10 strand=- repeatMasking=none
tgcttcctagGTCACACTTCACCTGAATCCCATCTCCTCAGTCCACATCC
ACCACAAGTCTGTTGTGTTCCTGCTCAACTCCCCACACCCCCTGGTGTGG
CATCTGAAGACAGAGAGACTTGCCACTGGGGTCTCCAGACTGTTTTTGgt
aagtgctt
>hg19_refGene_NM_001195683_3 range=chr1:92200323-92200526 5'pad=10 3'pad=10 strand=- repeatMasking=none
tttcctctagGTGTCTGAGGGTTCTGTGGTCCAGTTTTCATCAGCAAACT
TCTCCTTGACAGCAGAAACAGAAGAAAGGAACTTCCCCCATGGAAATGAA
CATCTGTTAAATTGGGCCCGAAAAGAGTATGGAGCAGTTACTTCATTCAC
CGAACTCAAGATAGCAAGAAACATTTATATTAAAGTGGGGGAAGgtaaat
ttta

id

NM_001195684    TGFBR3
NM_001206389    FGF8
NM_001197220    PDE4D
NM_001195683   TGFBR3

desired output value in bold updated with $2 in id because NM_ matched in $1 of id ,
value in italics added one to the 0 and the word exon

>hg19_refGene_TGFBR3_exon1 range=chr1:92327018-92327098 5'pad=10 3'pad=10 strand=- repeatMasking=none
agaaataaaaATGACTTCCCATTATGTGATTGCCATCTTTGCCCTGATGA
GCTCCTGTTTAGCCACTGCAGgtaagttgca
>hg19_refGene_TGFBR3_exon2 range=chr1:92262834-92263038 5'pad=10 3'pad=10 strand=- repeatMasking=none
cccttggcagGTCCAGAGCCTGGTGCACTGTGTGAACTGTCACCTGTCAG
TGCCTCCCATCCTGTCCAGGCCTTGATGGAGAGCTTCACTGTTTTGTCAG
GCTGTGCCAGCAGAGGCACAACTGGGCTGCCACAGGAGGTGCATGTCCTG
AATCTCCGCACTGCAGGCCAGGGGCCTGGCCAGCTACAGAGAGAGgtagg
tgcag
>hg19_refGene_TGFBR3_exon3 range=chr1:92224160-92224317 5'pad=10 3'pad=10 strand=- repeatMasking=none
tgcttcctagGTCACACTTCACCTGAATCCCATCTCCTCAGTCCACATCC
ACCACAAGTCTGTTGTGTTCCTGCTCAACTCCCCACACCCCCTGGTGTGG
CATCTGAAGACAGAGAGACTTGCCACTGGGGTCTCCAGACTGTTTTTGgt
aagtgctt
>hg19_refGene_TGFBR3_exon3 range=chr1:92224160-92224317 5'pad=10 3'pad=10 strand=- repeatMasking=none
tgcttcctagGTCACACTTCACCTGAATCCCATCTCCTCAGTCCACATCC
ACCACAAGTCTGTTGTGTTCCTGCTCAACTCCCCACACCCCCTGGTGTGG
CATCTGAAGACAGAGAGACTTGCCACTGGGGTCTCCAGACTGTTTTTGgt
aagtgctt
>hg19_refGene_TGFBR3_exon4 range=chr1:92200323-92200526 5'pad=10 3'pad=10 strand=- repeatMasking=none
tttcctctagGTGTCTGAGGGTTCTGTGGTCCAGTTTTCATCAGCAAACT
TCTCCTTGACAGCAGAAACAGAAGAAAGGAACTTCCCCCATGGAAATGAA
CATCTGTTAAATTGGGCCCGAAAAGAGTATGGAGCAGTTACTTCATTCAC
CGAACTCAAGATAGCAAGAAACATTTATATTAAAGTGGGGGAAGgtaaat
ttta

awk

awk 'NR==FNR{a[$1];next} {k=$2; sub(/_.*/,"",k)} k in a' file id
2

Hello cmccabe,

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

awk 'FNR==NR{A[$1]=$NF;next} {match($0,/NM_[0-9]+/);Q=substr($0,RSTART,RLENGTH);match($0,/NM_[0-9]+_[0-9]+/);W=substr($0,RSTART,RLENGTH);sub(/.*_/,X,W);if(Q && A[Q]){sub(Q"_",A[Q]"_exon",$0);sub(/exon[0-9]+/,"exon" ++W,$0);print;next};print}'  id  Input_file

Output will be as follows.

>hg19_refGene_TGFBR3_exon1 range=chr1:92327018-92327098 5'pad=10 3'pad=10 strand=- repeatMasking=none
agaaataaaaATGACTTCCCATTATGTGATTGCCATCTTTGCCCTGATGA
GCTCCTGTTTAGCCACTGCAGgtaagttgca
>hg19_refGene_TGFBR3_exon2 range=chr1:92262834-92263038 5'pad=10 3'pad=10 strand=- repeatMasking=none
cccttggcagGTCCAGAGCCTGGTGCACTGTGTGAACTGTCACCTGTCAG
TGCCTCCCATCCTGTCCAGGCCTTGATGGAGAGCTTCACTGTTTTGTCAG
GCTGTGCCAGCAGAGGCACAACTGGGCTGCCACAGGAGGTGCATGTCCTG
AATCTCCGCACTGCAGGCCAGGGGCCTGGCCAGCTACAGAGAGAGgtagg
tgcag
>hg19_refGene_TGFBR3_exon3 range=chr1:92224160-92224317 5'pad=10 3'pad=10 strand=- repeatMasking=none
tgcttcctagGTCACACTTCACCTGAATCCCATCTCCTCAGTCCACATCC
ACCACAAGTCTGTTGTGTTCCTGCTCAACTCCCCACACCCCCTGGTGTGG
CATCTGAAGACAGAGAGACTTGCCACTGGGGTCTCCAGACTGTTTTTGgt
aagtgctt
>hg19_refGene_NM_001195683_2 range=chr1:92224160-92224317 5'pad=10 3'pad=10 strand=- repeatMasking=none
tgcttcctagGTCACACTTCACCTGAATCCCATCTCCTCAGTCCACATCC
ACCACAAGTCTGTTGTGTTCCTGCTCAACTCCCCACACCCCCTGGTGTGG
CATCTGAAGACAGAGAGACTTGCCACTGGGGTCTCCAGACTGTTTTTGgt
aagtgctt
>hg19_refGene_NM_001195683_3 range=chr1:92200323-92200526 5'pad=10 3'pad=10 strand=- repeatMasking=none
tttcctctagGTGTCTGAGGGTTCTGTGGTCCAGTTTTCATCAGCAAACT
TCTCCTTGACAGCAGAAACAGAAGAAAGGAACTTCCCCCATGGAAATGAA
CATCTGTTAAATTGGGCCCGAAAAGAGTATGGAGCAGTTACTTCATTCAC
CGAACTCAAGATAGCAAGAAACATTTATATTAAAGTGGGGGAAGgtaaat
ttta

EDIT: Just going through your output again, not sure how the last 2 rows got the replacement in your output? As I can't see like string NM_001195683 , my code is not taking care of this as I am not sure how it has come over there, kindly explain it more so that we could try to help you on same.

EDIT2: Adding a non-one liner form of solution now too.

awk 'FNR==NR{
		A[$1]=$NF;
		next
            } 
            {
		match($0,/NM_[0-9]+/);
		Q=substr($0,RSTART,RLENGTH);
		match($0,/NM_[0-9]+_[0-9]+/);
		W=substr($0,RSTART,RLENGTH);
		sub(/.*_/,X,W);
		if(Q && A[Q]){
				sub(Q"_",A[Q]"_exon",$0);
				sub(/exon[0-9]+/,"exon" ++W,$0);
				print;
				next
			     };
		print
	    }
    ' id  Input_file

Thanks,
R. Singh

1 Like
3

Another way:

awk '
  {
    split($1,F,/_/)
  }
  NR==FNR {
    A[F[1],F[2]]=$2
    next
  } 
  (F[3],F[4]) in A {
    sub(F[3] "_" F[4] "_" F[5], A[F[3],F[4]] "_exon" F[5]+1)
  }
  {
    print RS $0
  }
' file RS=\> ORS= id

if you only want to print the ones that matched:

awk '
  {
    split($1,F,/_/)
  }
  NR==FNR {
    A[F[1],F[2]]=$2
    next
  } 
  (F[3],F[4]) in A {
    sub(F[3] "_" F[4] "_" F[5], A[F[3],F[4]] "_exon" F[5]+1)
    print RS $0
  }
' file RS=\> ORS= id
1 Like
4

Thank you both for your help. I fixed the typo in the id file as well as all the NM_ should be found. Thank you :).