Perl- matrix problem

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# 1  
Old 02-17-2009
Perl- matrix problem

A C G T -
A 5 -4 -4 -4 -5
C -4 5 -4 -4 -5
G -4 -4 5 -4 -5
T -4 -4 -4 5 -5
- -5 -5 -5 -5 0

So lets say I have a matrix which looks something like (above). Its basically a scoring matrix. the numbers are separated by columns are separated by tab and the lines are separated by well a line "\n". So I am trying to write a perl code that reads the file and stores the matrix in anything a list, an array or hash tables... I realize i need to use references but i could be wrong. I was wondering if someone could help me out... I wrote a global alignment program and now i was writing this code so say if i am looking up AA i get 5 if i was looking up TG i get -4
# 2  
Old 02-17-2009
Next time please use [code ][/code ] tags for pre-formatted text (output/code/...)
#!/usr/bin/perl -W

use strict;
use warnings;

my ( $FH, %data, @temp, $i, $line, @header );

$line = <DATA>;
chomp $line;
@header = split /\t/, $line;
while ( $line = <DATA> ) {
    chomp $line;
    @temp = split /\t/, $line;
    $data{ $temp[0] } = {};
    for ( $i = 1 ; $i <= $#temp ; $i++ ) {
        $data{ $temp[0] }{ $header[$i] } = $temp[$i];

print $data{'A'}{'A'}, "\n";
print $data{'T'}{'G'}, "\n";

        A       C       G       T       -
A       5       -4      -4      -4      -5
C       -4      5       -4      -4      -5
G       -4      -4      5       -4      -5
T       -4      -4      -4      5       -5
-       -5      -5      -5      -5      0

I'm using an inline file here, so you'll have to adapt it if you want the file from the command line or where ever. First key of %data is the row, second is the column.
# 3  
Old 02-20-2009
Thanks man that really helped thank you
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