You will have to do some sort of buffering of your input data. Your program read line-by-line and will not handle (by design) tags spanning multiple lines.
#!/usr/bin/perl -w
use strict;
my $text = do { local $/; <DATA> }; # read entire file
print $text;
$text =~ s/<B.*?ird>[^=+]*[=+]*\B//sg; # remove unwanted stuff
print $text;
__DATA__
(Example 1)
I have the following lines:
This is some text....<Bluebird>..
MBAAAEgAAAQAB
blaah,blaah
=+=+=+=+=+=+=+=+=+=+=+
(Example 2)
but sometimes it looks like this:
This is some text....<B
luebird>..MBAAAEgAAAQAoBA
AAQKAREDSCETRTBDFS
blaah,blaah
=+=+=+=+=+=+=+=+=+=+=+
And the output is as expected:
(Example 1)
I have the following lines:
This is some text....
(Example 2)
but sometimes it looks like this:
This is some text....
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