I have been working on a module that should do what you're looking for. Usage for your case follows, and the module is in the readmore tag below. Just put it in the same directory as your script and name it Permute.pm. Sorry no POD yet, but you should be able to get the idea.
use strict; use Permute; my $string = 'RAGGTS'; $string =~ s/S/\[C,G\]/g; $string =~ s/R/\[A,G\]/g; $string =~ s/K/\[G,T\]/g; # $string now becomes: [A,G]AGGT[C,G] my $seq = Permute->New($string); # get one at a time while (my $out = $seq->Next){ print "$out \n"; } # or all at once my @allofthem = $seq->All;
package Permute; # # String Permutation Expander # 11/15/2007 MF ver 0.04 # use strict; sub New{ my $class = shift; my $string = shift; my %options = @_; my $self = {}; bless ($self, $class); if (ref($options{marker}) eq "ARRAY" and $options{marker}[0] ne $options{marker}[0]){ $self->{Smark} = $options{marker}[0]; $self->{Emark} = $options{marker}[1]; }elsif( defined $options{marker} ){ warn "Invalid Marker Option"; return; }else{ $self->{Smark} = '['; $self->{Emark} = ']'; } $self->_parse($string); return $self; } sub Next{ my $obj = shift; $obj->_index(+1); return $obj->Read; } sub Prev{ my $obj = shift; if ($obj->{ci} == 0){ $obj->{ci} = $obj->{mi}; $obj->_sync; }else{ $obj->_index(-1); } return $obj->Read; } sub Read{ my $obj = shift; if ($obj->{ci} == 0){ return; } my $red; for ( @{ $obj->{blob} } ){ $red .= "$_->[0][ $_->[1] ]"; } return $red; } sub GetIndex{ return $_[0]->{ci}; } sub GetCount{ return $_[0]->{mi}; } sub SetIndex{ my ($obj, $newidx) = @_; unless ($newidx =~ /^\d+$/ and $newidx <= $obj->{mi}){ return; } $obj->{ci} = $newidx; $obj->_sync; return 1; } sub Reset{ $_[0]->{ci} = 0; } sub All{ my $obj = shift; $obj->{saveidx} = $obj->GetIndex; $obj->Reset; my @all; my $string; while ($string = $obj->Next){ push(@all, $string) } $obj->SetIndex($obj->{saveidx}); if (wantarray){ return @all; } return \@all; } # separates string and iteration segments sub _parse{ my ($obj, $string) = @_; my ($S, $E) = ($obj->{Smark}, $obj->{Emark}); my @accum; $obj->{ci} = 0; $obj->{mi} = 1; while(defined $string){ my ($pre, $remain) = split(/\Q$S/o, $string, 2); if (defined $pre){ push(@accum, [ [$pre], 0, 1 ]); } my ($perm, $post) = split(/\Q$E/o, $remain, 2); if (defined $perm){ my $subaref = _expand($perm); push(@accum, [ $subaref, 0, scalar(@$subaref) ]); $obj->{mi} *= scalar @$subaref; } $string = $post; } $obj->{blob} = \@accum; } # expands iteration segments into array sub _expand{ my @block = split(/\s*,\s*/, shift); my @acc; for (@block){ if ($_ =~ /^\'(.+)\'$/) { push(@acc, $1) } elsif ($_ =~ /^\"(.+)\"$/) { push(@acc, $1) } elsif ($_ =~ /^(\d+)\.\.(\d+)$/) { push(@acc, _seq($1, $2)) + } elsif ($_ =~ /^([a-z])\.\.([a-z])$/){ push(@acc, _seq($1, $2)) + } elsif ($_ =~ /^([A-Z])\.\.([A-Z])$/){ push(@acc, _seq($1, $2)) + } else { push(@acc, split(/\s+/, +$_)) } } return \@acc; } # expands num/character sequences sub _seq{ my ($beg, $end) = @_; if ($end lt $beg){ my $str = qq("$end".."$beg"); return reverse eval $str; }else{ my $str = qq("$beg".."$end"); return (eval "$str"); } } # increment or decrement the object index sub _index{ my ($obj, $incr) = @_; $obj->{ci} += $incr; if ($obj->{ci} < 0){ $obj->{ci} = $obj->{mi}; }elsif ($obj->{ci} > $obj->{mi}){ $obj->{ci} = 0; } if ($obj->{ci}){ $obj->_sync; } } # synchronize object index with iteration array indexes sub _sync{ my $obj = shift; my $ai = $obj->{ci} - 1; for my $seg (reverse @{ $obj->{blob} }){ if ($seg->[2] == 1){ next } $seg->[1] = $ai % $seg->[2]; $ai = int($ai / $seg->[2]); } } 1; __END__
In reply to Re: How to expand a string
by hangon
in thread How to expand a string
by Anonymous Monk
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