print $new $l;
[download]

perl -le '$x="foo"; $y="bar"; print $x $y'

perl -le '$x="foo"; $y="bar"; print $x, $y'
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perl -wle '$x="foo"; $y="bar"; print $x $y'
print() on unopened filehandle foo at -e line 1.
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Sorry - total brain fart on on the stuff above. I forgot that $new was supposed to be a file handle. Oh well.

UPDATE: Random Walk has apparently solved your problem, but here's a slightly different version of the same solution anyway... (possibly a bit less different from the OP code, possibly a little simpler, and, well, at least this allows my reply to have some usable content):

use strict;
use warnings;

my $name = "name";

# open( my $rfh,'<', $entry ) or die "cannot open > $entry: $!";
open( my $new, '>', "$name\_new.txt" ) or die "cannot open: $!";

my $signal1 = "s_abc_out";
my $signal2 = "s_abc_in";
my $label = "label";

while ( <DATA> ) {  # would be <$rfh> for you
    if ( /$signal2\(\d+\).*\s*<=\s*$signal1\(\d+\).*/ ) {
        for my $i ( 0 .. 6 ) {
            my $j = $i + 1;
            print $new "$signal2\_rrfa_$label($j) <= $signal1\_rrfa_$l
+abel($i);\n";
        }
    }
    else{
        print $new $_; 
    }
}

__DATA__
.................................
s_abc_in(1450) <= s_abc_out(324);
s_abc_in(1451 <= s_abc_out(1450);
.................................
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