awk to compare value of sub-string in field - awk

Question

In the below awk I am trying to extract and compare each substring in $4 that stars with p.. If the first three letters is the same as the last three (there is a digit in between) then that p. is updated to p.(3 letters)(digit)(=) --- the () are only to show that there are 3 enteries and are not needed. If the 3 letters are different then that line is unchanged. In the below file line 1 in an example. In my actual data there are about 10,000 rows wth about 50 columns, but $4 is the only one that will have these values in ut, that is te p. The format of the p. will always be three letters followed by a 1-4 digit # followed by 3 more letters. The awk attempt below I think will extract each p. and split on the ;, but I am not sure how to compare to check if the three letters are the same. Thank you :).
file tab-delimited
Chr Start ExonicFunc.refGene AAChange.refGene
chr1 155880573 synonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu110Glu;RIT1:NM_001256822:exon2:c.31G>C:p.Glu110Glu
chr1 155880573 nonsynonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu11Gln
desired output tab-delimited
Chr Start ExonicFunc.refGene AAChange.refGene
chr1 155880573 synonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu110=;RIT1:NM_001256822:exon2:c.31G>C:p.Glu110=
chr1 155880573 nonsynonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu11Gln
awk
awk '
BEGIN { OFS="\t" }
$4 ~ /:NM/ {
ostring=""
# split $4 by ";" and cycle through them
nNM=split($4,NM,";")
for (n=1; n<=nNM; n++) {
if (n>1) ostring=(ostring ";") # append ";"
if (match(NM[n],/p[.].*/)) {
# copy up to "p."
ostring=(ostring substr(NM[n],1,RSTART+1))
# Get the substring after "p."
VAL=substr(NM[n],RSTART+2)
# Get its length
lenVAL=length(VAL)
# store aa array
aa=[{while(length($4)=3){print substr($044,1,3);gsub(/^./,"")}]}' file

Answer 1

Extended GNU awk solution:
awk 'NR==1; NR > 1{
len = split($4, a, /\<p\.[a-zA-Z]{3}[0-9]+[a-zA-Z]{3}\>/, seps);
if (len == 1){ print; next }
res = ""
for (i=1; i < len; i++) {
s = seps[i];
if (substr(s, 3, 3) == substr(s, length(s) - 2)) {
seps[i] = substr(s, 1, length(s) - 3)"=";
}
}
for (i=1; i <= len; i++)
res = res a[i] (seps[i]? seps[i]:"");
$4 = res; print
}' FS='\t' OFS='\t' file
The output:
Chr Start ExonicFunc.refGene AAChange.refGene
chr1 155880573 synonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu110=;RIT1:NM_001256822:exon2:c.31G>C:p.Glu110=
chr1 155880573 nonsynonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu11Gln
Time performance measurement:
Input testfile:
$ wc -l testfile
10000 testfile
time(awk 'NR==1; NR > 1{
len = split($4, a, /\<p\.[a-zA-Z]{3}[0-9]+[a-zA-Z]{3}\>/, seps);
if (len == 1){ print; next }
res = ""
for (i=1; i < len; i++) {
s = seps[i];
if (substr(s, 3, 3) == substr(s, length(s) - 2)) {
seps[i] = substr(s, 1, length(s) - 3)"=";
}
}
for (i=1; i <= len; i++)
res = res a[i] (seps[i]? seps[i]:"");
$4 = res; print
}' FS='\t' OFS='\t' testfile >/dev/null)
real 0m0.269s
user 0m0.256s
sys 0m0.000s
time(awk 'BEGIN { FS=OFS="\t" }
NR>1 {
head = ""
tail = $4
while ( match(tail,/(p\.([[:alpha:]]{3})[0-9]+)([[:alpha:]]{3})/,a) ) {
head = head substr(tail,1,RSTART-1) a[1] (a[2] == a[3] ? "=" : a[3])
tail = substr(tail,RSTART+RLENGTH)
}
$4 = head tail
}
{ print }' testfile >/dev/null)
real 0m0.470s
user 0m0.416s
sys 0m0.008s

Answer 2

With GNU awk for the 3rd arg to match():
$ cat tst.awk
BEGIN { FS=OFS="\t" }
NR>1 {
head = ""
tail = $4
while ( match(tail,/(p\.([[:alpha:]]{3})[0-9]+)([[:alpha:]]{3})/,a) ) {
head = head substr(tail,1,RSTART-1) a[1] (a[2] == a[3] ? "=" : a[3])
tail = substr(tail,RSTART+RLENGTH)
}
$4 = head tail
}
{ print }
$ gawk -f tst.awk file
Chr Start ExonicFunc.refGene AAChange.refGene
chr1 155880573 synonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu110=;RIT1:NM_001256822:exon2:c.31G>C:p.Glu110=
chr1 155880573 nonsynonymous SNV RIT1:NM_001256821:exon2:c.31G>C:p.Glu11Gln