I assume the program has directory $wDir as its current working directory, and $transFile starts with the directory part "docTmp/coded/".

If the target directory .../tmp is not present, the file to be moved will be placed in the parent directory instead and will be renamed to tmp. So I would make sure beforehand that the target directory exists.

For the creation of directories of any depth, use mkpath() from core module File::Path. For moving you could use Perl's File::Copy module. It has a portable move() function. I would do it like this (untested):

# read trans barcode 
$primer = Util::Util::trim(Util::Util::fileDecode($transFile));

# set transaction folder path
my $transPath = "plsTrans/" . $primer . "/tmp/";

use File::Path qw(mkpath);
# create the target directory if there is none
if (!-d $transPath) {
    mkpath $transPath or die "cannot create target directory $transPat
+h:$!\n";
}

use File::Copy qw(move);
move($transFile, $transPath . $transFile)
    or die "move to $transPath failed: $!";
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