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use strict;
use warnings;
...
Output:
-------
"Transcription factor",promoter,DNA,"Transcription factor",promoter,DN
+A.

$str =~ s/((?:(?!\").)*)(\"[^\"]+\")((?:(?!\").)*)/
my $fi = $1;my $se = $2; my $th = $3;
$fi =~ s| |\,|g;$th =~ s| |\,|g;
"$fi$se$th"/egs;