Re: Calculating values of a 2d array by comparison of 2 strings

"Pepetideo" <pepetideo@xxxxxxxxxxx> wrote:
anno4000@xxxxxxxxxxxxxxxxxxxxxx wrote:
Pepetideo <pepetideo@xxxxxxxxxxx> wrote in comp.lang.perl.misc:
Hi. I am having a hard time dealing with a problem And I was wondering
if anyone has a suggestion to how I should do this.

I have 2 strings that I want to compare. These strings are composed of
amino acid residues (long sequences of any of 20 characters) these
string are aligned to each other and I want to compare each position of
the two strings and fill up a matrix of 21*21 so that for eg:

AAAAAA....
ATLL_Y....

1 pos: A-A -> counts 1 and adds to position [0][0] on the matrix
2 pos: A-T -> counts 1 and adds to position [0][1] on the matrix
3 pos: A-L -> counts 1 and adds to position [0][2] on the matrix
4 pos: A-L -> counts 1 and adds to position [0][2] on the matrix
5 pos: A-_ -> counts 1 and adds to position [0][21] on the matrix
6 pos: A-Y -> counts 1 and adds to position [0][10] on the matrix
...

I've been suggested by a friend to use a switch but this ends up needing
441 cases of assignments in other to fill up every position of the matrix.

Does anyone know of a better way of dealing with this? I appreciate any
suggestions. Thanks

Probably. Use a two-dimensional hash to count the combinations
directly, without mapping the letters to array indices. Here is how:

my $str1 = 'AAAAAA';
my $str2 = 'ATLL_Y';

my %count;

my @str1 = split //, $str1;
my @str2 = split //, $str2;

for my $ch1 ( @str1 ) {
my $ch2 = shift @str2;
++ $count{ $ch1}->{ $ch2};
}

# example:
print "The count for 'A' and 'L' is $count{ A}->{ L}\n";

If you do need the array form you can generate it from the count hash.


Thank you very much for the suggestion... I think this is a good idea...
My doubt is that I am going this to many sequences and the arrays have
positions have to be the same... in order th convert the count ashe to
the matrix would i not need to create 431 assignment statements like :

@matrix[0][0] = $count{a}->{l};


Maybe not... Here's a variation on Anno's method. I assume you have a list
of characters; from your example, we know that A is 0, T is 1, etc. Make a
string of the characters where each character's position in the string is
the same as its index in the matrix. From the string of characters, make a
hash that maps each character to its index. Then count in @matrix.

I think this is the same as Anno's idea of generating the matrix from the
count hash, but it shortcuts the creation of the hash using the characters
from your amino acid residues.

my $chars = 'ATL-------Y----------_';

my $i = 0;
my %chNdx = map { $_ => $i++ } split //, $chars;

my $str1 = 'AAAAAA';
my $str2 = 'ATLL_Y';

my @matrix;

my @ndx1 = map { $chNdx{$_} } (split //, $str1);
my @ndx2 = map { $chNdx{$_} } (split //, $str2);

for my $i (@ndx1) {
my $j = shift @ndx2;
++ $matrix[$i][$j];
}

Mark

.

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