in reply to Perl regular expression for amino acid sequence

#! perl -slw
use strict;

my $s = 'XXQQGGYYNNQGYNNNNQNGGNGGNGGGQQQNNN';

print $s; 
print ' ' x( pos( $s ) - length( $1) ), $1 
    while $s =~ m[
        (                     ## Capture to $1
        
            (?:             ## A group
                ([QGYN])    ## of these characters
                (?!\2{2})   ## repeated no more than twice in successi
+on
            ){3,6}          ## 3 to 6 characters in length
            ?                 ## Remove for greedy matching.    
        )
]xg;

## Condensed and greedy
print $s; 
print ' ' x( pos( $s ) - length( $1) ), $1 
    while $s =~ m[( (?: ([QGYN]) (?!\2{2}) ){3,6} ) ]xg;

__END__
[20:37:58.32] P:\test>temp
XXQQGGYYNNQGYNNNNQNGGNGGNGGGQQQNNN
  QQG
     GYY
        NNQ
               NNQ
                  NGG
                     NGG
XXQQGGYYNNQGYNNNNQNGGNGGNGGGQQQNNN
  QQGGYY
        NNQGY
               NNQNGG
                     NGGN

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Examine what is said, not who speaks.
"But you should never overestimate the ingenuity of the sceptics to come up with a counter-argument." -Myles Allen
"Think for yourself!" - Abigail        "Time is a poor substitute for thought"--theorbtwo         "Efficiency is intelligent laziness." -David Dunham
"Memory, processor, disk in that order on the hardware side. Algorithm, algorithm, algorithm on the code side." - tachyon

Replies are listed 'Best First'.
Re^2: Perl regular expression for amino acid sequence
by ikegami (Patriarch) on Dec 01, 2004 at 21:04 UTC

    Your code returns

    xxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
       NNG
          YGY
                    GYG
                                   NNG
xxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
       NNGYGY
                    GYGY
                                   NNG

    [download]

    whereas I would have expected

    xxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
       NNGYGY
                    GYGYNN
                                   NNGNN

    [download]
[reply]
[d/l]
[select]

      I didn't read the question that way, but now you've pointed it out, yours could be, and probably is the more correct interpretation.

      If the regex engine wouldn't insist that, any reference to a previous capture, in a negative look-behind assertion, *must* be variable length (and therefore disallowed), even when the brackets referenced can only, and must, capture exactly one char.

      Then it would be easy to fix this to meet your interpretation of the problem. Alas it does, so there isn't :)

      I cannot see fix at the moment.

      Examine what is said, not who speaks.
      "But you should never overestimate the ingenuity of the sceptics to come up with a counter-argument." -Myles Allen
      "Think for yourself!" - Abigail        "Time is a poor substitute for thought"--theorbtwo         "Efficiency is intelligent laziness." -David Dunham
      "Memory, processor, disk in that order on the hardware side. Algorithm, algorithm, algorithm on the code side." - tachyon
[reply]
        There's a neat trick to get around the lookbehind-thinks-backreferences-are-variable-length problem: embed a lookahead in your lookbehind. It doesn't mind if you use backreferences inside the lookahead.

        For the problem at hand, it would go like this 

            /([QGYN]{2}   # First two characters of the desired class
      (?:          # Followed by the complex expression...
        # Look for a trio starting two characters back
        (?<=(?!(.)\2\2)..)
        [QGYN]     # Then take another of the desired class
      ){1,4}       # ...1 to 4 times
      )/gx

        [download]
        This was a trick someone posted some time ago, but it was over my head at the time. Now I get it.
        Caution: Contents may have been coded under pressure.
[reply]
[d/l]

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