R extract part of string

Question

I have a question about extracting a part of a string. For example I have a string like this:

a <- "DP=26;AN=2;DB=1;AC=1;MQ=56;MZ=0;ST=5:10,7:2;CQ=SYNONYMOUS_CODING;GN=NOC2L;PA=1^1:0.720&2^1:0"

I need to extract everything between GN= and ;.So here it will be NOC2L.

Is that possible?

Note: This is INFO column form VCF file format. GN is Gene Name, so we want to extract gene name from INFO column.

Answer 1

Try this:

sub(".*?GN=(.*?);.*", "\\1", a)
# [1] "NOC2L"

Answer 2

Assuming semicolons separate your elements, and equals signs occur exclusively between key/value pairs, a non-strictly-regex method would be:

bits <- unlist(strsplit(a, ';'))
do.call(rbind, strsplit(bits, '='))

      [,1] [,2]               
 [1,] "DP" "26"               
 [2,] "AN" "2"                
 [3,] "DB" "1"                
 [4,] "AC" "1"                
 [5,] "MQ" "56"               
 [6,] "MZ" "0"                
 [7,] "ST" "5:10,7:2"         
 [8,] "CQ" "SYNONYMOUS_CODING"
 [9,] "GN" "NOC2L"            
[10,] "PA" "1^1:0.720&2^1:0"  

Then it's just a matter of selecting the appropriate element.

Answer 3

One way would be:

gsub(".+=(\\w+);.+", "\\1", a, perl=T)

I am sure there are more elegant ways to do it.