Perhaps those "blank" lines contain spaces? Also, using chomp simply removes line endings (e.g. carriage return), it won't skip to the next line. You haven't really shown us your code, but presumably you need something like:

#!/usr/bin/perl -w

use strict;

while (<>)
{
    # loop to next line if it contains whitespace only
    next if /^\s+$/;

    print;
}
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Update: Tested with files with blank lines consisting of just \n and blank lines with spaces; works in both cases; \s+ matches end-of-line characters, see perlretut (query from mirod & busunsl).

Change

next if /^\s+$/;
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to

next if /^\s*$/;
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and it will catch empty lines and lines containing only whitespace.

Actually Perl DWIMs properly here, and /^\s+$/ catches empty lines. The $ is quite magic, if the \n at the end of the string/line is matched then $ matches the empty end-of-string, if the \n is not matched then $ matches it, plus the end-of-string.

You can test it with this code:

my $string="12\n";
print 'matches ^\d+\n$' . "\n" if( $string=~ /^\d+\n$/);
print 'matches ^\d+$' . "\n"   if( $string=~ /^\d+$/);
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--
Steve Marvell

To shorten your logic a bit:

perl -ni.bak -e 'print if /\S/' file1 file2 ...

In other words, "print if there is non-whitespace" versus "print unless composed of only whitespace".

Update:To the benefit of speed too:

#!/usr/bin/perl -w

use strict;
use Benchmark qw(timethese);

my @data = ("sponge\n","\n",
   "wibble\n","boing\n",
   "spam\n","\n"," spud\n"); 

my $nsre = qr/\S/;
my $isre = qr/^\s+$/;

timethese(1E6, {
   'nospace' => sub { grep {/$nsre/} @data; },
   'isspace' => sub { grep {!/$isre/} @data; }})
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Resulting in:

Benchmark: timing 1000000 iterations of isspace, nospace...
   isspace: 67 wallclock secs (56.34 usr +  0.15 sys = 56.49 CPU) @ 17
+702.25/s (n=1000000)
   nospace: 63 wallclock secs (49.19 usr +  0.26 sys = 49.45 CPU) @ 20
+222.45/s (n=1000000)
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Unless my dataset is unfair.

--
¤ Steve Marvell

--
John.

#!/usr/bin/perl -w

use strict;

while (<>) {
    next if (/^\n/);
    print;
}
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next if (/^\s*$/);
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