Re^2: Finding Consensus String

Dear japhy,
Thanks so much for your answer to my posting. I just have a question. Your code works well in generalize version of array like this:

my @instances = ( 'AAAAA  ATCGA',
                  'ATCGA  AAAAA',
                  'ATAAA  AAAAA',
                 );
[download]

But how can I make it more generalize for cases like this?

my @instances2 = ( 'AAAAA  ATCGA',
                   'ATCGA',
                   'ATAAA  AAAAA',
                 );
# consensus :       ATAAA  A[AT][CA][GA]A
[download]

Or this:

my @instances3 = ( 'AAAAA  ATCGA TTTT',
                   'ATCGA        TATA ',
                   'ATAAA  AAAAA ATTA ',
                 );
# consensus :      ATAAA  A[AT][CA][GA]A TTTA
[download]

Cause, currently it gives warning when encountering two cases like that.

Regards,
Edward

Comment on Re^2: Finding Consensus String Select or Download Code

Replies are listed 'Best First'.
Re^3: Finding Consensus String by japhy (Canon) on Oct 19, 2005 at 19:18 UTC
I don't get any warnings. What I do notice is that space is included in the `[...]` parts. So here's a small fix: `sub consensus { ... # code from before, until: # store only those who occur the most times my @most = grep $freq{$_} == $max, keys %freq; @most = grep $_ ne " ", @most if @most > 1; push @cons, \@most; } return \@cons; }` [download] And to get the string version, I use: `sub consensus_to_string { my $con = shift; my $str; for (@$con) { if (@$_ > 1) { $str .= "[" . join("", @$_) . "]" } else { $str .= $_->[0] } } return $str; }` [download] Jeff `japhy` Pinyan, P.L., P.M., P.O.D, X.S.: Perl, regex, and `perl` hacker How can we ever be the sold short or the cheated, we who for every service have long ago been overpaid? ~~ Meister Eckhart	[reply] [d/l] [select]

Replies are listed 'Best First'.

Re^3: Finding Consensus String
by japhy (Canon) on Oct 19, 2005 at 19:18 UTC

[...]

sub consensus {
  ... # code from before, until:

    # store only those who occur the most times
    my @most = grep $freq{$_} == $max, keys %freq;              
    @most = grep $_ ne " ", @most if @most > 1;
    push @cons, \@most;
  }

  return \@cons;
}
[download]

sub consensus_to_string {
  my $con = shift;
  my $str;

  for (@$con) {
    if (@$_ > 1) { $str .= "[" . join("", @$_) . "]" }
    else { $str .= $_->[0] }
  }

  return $str;
}
[download]

Jeff japhy Pinyan, P.L., P.M., P.O.D, X.S.: Perl, regex, and perl hacker
How can we ever be the sold short or the cheated, we who for every service have long ago been overpaid? ~~ Meister Eckhart

[reply]
[d/l]
[select]