Re^2: Bioinformatics: Regex loop, no output

[AnomalousMonk]

As BrowserUk pointed out here, there is no  ! regex metacharacter/operator (presumably meaning "not-followed-by-the-following-pattern"). What is probably meant is  (?!pattern) (see Look-Around Assertions in perlre; also see perlretut).

This may be what TamaDP was looking for (there are some other good solutions):

c:\@Work\Perl\monks>perl -wMstrict -le
"my @proteins = qw(
   DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG
   ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD
   AAAKAAA  AAAKAAA  XXXXXX
   );
 ;;
 my @new_peptides;
 for my $protein (@proteins) {
   if ($protein =~ s{ (?<= [KR]) (?! P) }{=}xmsg) {
     push @new_peptides, split ('=', $protein);
     }
   }
 ;;
 for my $peptide (@new_peptides) {
   print qq{Peptide is '$peptide'};
   }
"
Peptide is 'DAAAAATTLTTTAMTTTTTTCK'
Peptide is 'MMFRPPPPPGGGGGGGGGGGG'
Peptide is 'ALTAMCMNVWEITYHK'
Peptide is 'GSDVNR'
Peptide is 'R'
Peptide is 'ASFAQPPPQPPPPLLAIKPASDASD'
Peptide is 'AAAK'
Peptide is 'AAA'
Peptide is 'AAAK'
Peptide is 'AAA'

Un-s///-ubstituted input proteins are not split and push-ed into the output array.

Yet another solution might be:

c:\@Work\Perl\monks>perl -wMstrict -le
"my @proteins = qw(
   DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG
   ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD
   AAAKAAA  AAAKAAA  XXXXXX
   );
 ;;
 my $cleave = qr{ (?<= [KR]) (?! P) }xms;
 ;;
 my @peptides =
   map  split($cleave),
   grep m{ $cleave }xms,
   @proteins
   ;
 ;;
 print qq{Peptide is '$_'} for @peptides;
"
Peptide is 'DAAAAATTLTTTAMTTTTTTCK'
Peptide is 'MMFRPPPPPGGGGGGGGGGGG'
Peptide is 'ALTAMCMNVWEITYHK'
Peptide is 'GSDVNR'
Peptide is 'R'
Peptide is 'ASFAQPPPQPPPPLLAIKPASDASD'
Peptide is 'AAAK'
Peptide is 'AAA'
Peptide is 'AAAK'
Peptide is 'AAA'

in which the central process might be documented (with the steps of the statement being taken right-to-left, bottom-to-top) as:

my @peptides =           # 4. and the pieces are peptides.
  map  split($cleave),   # 3. split at each cleavage point...
  grep m{ $cleave }xms,  # 2. that can be cleaved, ...
  @proteins              # 1. for each protein...
  ;

Update: After sober consideration, I changed the code example above to its present form. The previous code contained
    my $cleave = qr{ [KR] (?! P) }xms;
    ...
      map  split(m{ (?<= $cleave) }xms),
      grep m{ $cleave }xms,
      ...
which doesn't really respect the DRY principle, which is what I was aiming to exemplify.