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Hi,

I am looking for an elegant way to do the union of two string. For
example:

$seq1 = "--- --- GAA --- GGA";
$seq2 = "AAC TGG --- --- ---";

The rule is to do the union of the letters, leaving the dash symbol
when both have a dash in a given position:

$union = "AAC TGG GAA --- GGA";

Anyone? Maybe using a regular expression?

Thanks,

Albert.

avilella <> writes:

> Hi,
>
> I am looking for an elegant way to do the union of two string. For
> example:
>
> $seq1 = "--- --- GAA --- GGA";
> $seq2 = "AAC TGG --- --- ---";
>
> The rule is to do the union of the letters, leaving the dash symbol
> when both have a dash in a given position:
>
> $union = "AAC TGG GAA --- GGA";

Perhaps:

$seq1 =~ s/-/substr($seq2, pos($seq1), 1)/eg;

Works for your test case. Perhaps you have more data to test it
against?

Cheers,
Danny.

avilella <> wrote:
>I am looking for an elegant way to do the union of two string. For
>example:
>
>$seq1 = "--- --- GAA --- GGA";
>$seq2 = "AAC TGG --- --- ---";
>
>The rule is to do the union of the letters, leaving the dash symbol
>when both have a dash in a given position:
>
>$union = "AAC TGG GAA --- GGA";
>
>Anyone? Maybe using a regular expression?

Sometimes just using different terminology solves the mysterie:

In sequence 1 (logically those are not strings but as you indicated
yourself they are sequences) you want to replace each '---' element with
the corresponding element from sequence 2.

#untested, sketch only
my @a = split(/ /, $seq1);
my @b = split(/ /,$seq2);
for my $i (0..$#a) {
if ($a[i] eq '---') {$a[i] = $b[i]};
}
my $res = join (' ', @a);

This can probably be optimized somewhat by using map() and computing the
result elements in the argument of the join() but this way the logic is
very accessible.

jue

On Sep 21, 9:12*am, avilella <avile...@gmail.com> wrote:
> Hi,
>
> I am looking for an elegant way to do the union of two string. For
> example:
>
> $seq1 = "--- --- GAA --- GGA";
> $seq2 = "AAC TGG --- --- ---";
>
> The rule is to do the union of the letters, leaving the dash symbol
> when both have a dash in a given position:
>
> $union = "AAC TGG GAA --- GGA";

I would approach this from the standpoint of comparing arrays rather
than looking at strings. Split each sequence and then iterate through
the arrays.

use strict;
use warnings;
my $s1 = "--- --- GAA --- GGA";
my $s2 = "AAC TGG --- --- ---";
my @s1 = split / /, $s1;
my @s2 = split / /, $s2;
my @s3 = ();
my $len = @s1; #get the length
for (my $i = 0; $i < $len; $i++)
{
$s3[$i] = '---' if $s1[$i] eq '---' and $s2[$i] eq '---';
$s3[$i] = $s1[$i] if $s1[$i] =~ /[A-Z]{3}/ and $s2[$i] eq '---';
$s3[$i] = $s2[$i] if $s1[$i] eq '---' and $s2[$i] =~ /[A-Z]{3}/;
$s3[$i] = '***' if $s1[$i] =~ /[A-Z]{3}/ and $s2[$i] =~ /[A-Z]{3}/;
}
my $s3 = join ' ', @s3;
print $s3;
exit(0);