正则表达式仅在不匹配其他模式时才匹配特定模式

Question

I need to create a matching regex to find genetic sequences and I got stuck behind one specific problem - after first, start codon ATG , follows other codons from three nucleotides as well and the regex ends with three possible codons TAA , TAG and TGA . What if the stop(end) codon goes after the start( ATG ) codon? My current regex works when there are intermediate codons between start and stop codon, but if there are none, the regex matches ALL of the sequence after start codon. I know why it does that, but I have no idea how to change it to work the way I want it to.

My regex should look for AGGAGG (exactly this pattern), then A , C , G or T (from 4 to 12 times) then ATG (exactly this pattern), then A , C , G or T (in triples (for example, ACG , TGC and etc.), doesn't matter how long) UNTIL it matches TAA , TAG or TGA . The search should end after that and start again after that.

Example of a good match:

XXXXXXXXXXXXXXXXXXXXXXXXX   XXXXXXXXXXXXXXXX
AGGAGGTATGATGCGTACGGGCTAGTAGAGGAGGTATGATGTAGTAGCATGCT

There are two matches in the sequence - from 0 to 25 and from 28 to 44.

My current regex(don't mind the first two brackets):

$seq =~ /(AGGAGG)([ACGT]{4,12})(ATG)([ACTG]{3,3}){0,}(TAA|TAG|TGA)/ig

Answer 1

Problem here comes from the default usage of greedy quantifiers.

When using (AGGAGG)([ACGT]{4,12})(ATG)([ACTG]{3})*(TAA|TAG|TGA) , 4th group ([ACTG]{3})* will match as many as possible, then only 5th group is considered (backtracking if needed).
In your sequence you get TAGTAG . Greedy quantifier will lead to first TAG being captured in group 4, and second one captured as ending group.

You may use lazy quantifier instead: (AGGAGG)([ACGT]{4,12})(ATG)([ACTG]{3})*?(TAA|TAG|TGA) (note the added question mark, making the quantifier lazy).
That way, first TAG encountered will be treated as the ending group.

Demo .

Answer 2

According to the pattern you gave, you could have overlapping matches. The following will find all matches, including overlapping matches:

local our @matches;
$seq =~ /
   (
   ( AGGAGG )
   ( [ACGT]{4,12} )
   ( ATG )
   ( (?: (?! TAA|TAG|TGA ) [ACTG]{3} )* )
   ( TAA|TAG|TGA )
   )
   (?{ push @matches, [ $-[1], $1, $2, $3, $4, $5, $6 ] })
   (?!)
/xg;

Answer 3

Perl essential regex feature, as opposed to plain regex like grep, is the lazy quantifier: ? following the * or + quantifier. it matches zero (one) or more occurrence of the character preceding * (+) token as the shortest glob match as possible

$seq =~ /((AGGAGG)([ACGT]{4,12})(ATG)([ACGT]{3})*?(TAA|TAG|TGA))/igx