print "$1, $2, $3\n"
              while $line =~ /GI=(\d+),(\w+),(\d+\-\d+)/g;
[download]

Hi neversaint,

You have to add while statement to get all the matches.

use strict;
use warnings;
use Data::Dumper;

my %all_entry;

while (<DATA>) {    
        chomp;           
        next unless (/^>/);       
        my $line = $_;   

    while ($line =~ /GI\=(\d+)\,(\w+)\,(\d+\-\d+)/g){        
                    
    push @{ $all_entry{$1}{$2} }, $3;
                    
    }
        
        

    }

print Dumper \%all_entry;

output:
-------

$VAR1 = {
          '162960844' => {
                           'bw' => [
                                     '0-4',
                                     '9025576-9025608'
                                   ]
                         },
          '152989753' => {
                           'bw' => [
                                     '0-30',
                                     '1877925-1877931'
                                   ]
                         }
        };
[download]

        # 'g' doesn't seem to work
[download]

It doesn't work since there is only one pair of curly braces per line. Also, a m//g in scalar context matches once and sets the position for further matches at the end of the match (see pos).

$_ = ">r7.1 |SOURCES={GI=162960844,bw,0-4;GI=162960844,bw,9025576-9025
+608}|";
$_ =~ /GI=(\d+),(\w+),(\d+\-\d+)/g;
print "$_\n";
print "-" x pos(),"^\n";
print pos(),"\n";
__END__
>r7.1 |SOURCES={GI=162960844,bw,0-4;GI=162960844,bw,9025576-9025608}|
-----------------------------------^
35
[download]

If you want to match the stuff inside the curlies and then build your structure from multiple matches, you need two passes - first isolate what's inside the curlies, then match with m//g:

use Data::Dumper;
my %all_entry;
while (<DATA>) {
    chomp;
    next unless (/^>/);

    my ($line) = />.*\{((?:GI=\d+,\w+,\d+\-\d+;?)+)\}/;

    push @{ $all_entry{$1}{$2} }, $3
        while $line =~ /GI=(\d+),(\w+),(\d+\-\d+)/g;
}

print Dumper \%all_entry;
__DATA__
>r7.1 |SOURCES={GI=162960844,bw,0-4;GI=162960844,bw,9025576-9025608}|
>r6.1 |SOURCES={GI=152989753,bw,0-30;GI=152989753,bw,1877925-1877931}|
[download]