# slurp in file into a string
$/=''; $DNA = <FILE>; 
# remove \n at end
chomp($DNA);

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You have set $/ to paragraph mode so it will not "slurp in file", just the first paragraph of the file.    Also the value of $/ will effect what chomp removes (hint: paragraph mode removes more than just a single \n character). 



# replace line endings with commata
$DNA =~ s/\n/,/;

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That replaces a single newline.    If you want to replace ALL newlines then: 

# replace newlines with commas
$DNA =~ s/\n/,/g;

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Or perhaps: 

# replace newlines with commas
$DNA =~ tr/\n/,/;

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In reply to Re^2: How can one get all possible combinations of elements of different arrays using File::Glob(bsd_glob)? by jwkrahn
in thread How can one get all possible combinations of elements of different arrays using File::Glob(bsd_glob)? by supriyoch_2008

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