Highlight a table row with a rectangular overlay

You could put the \input in a node and draw a rectangle relative to the corners of the node.

\begin{filecontents*}{table.tex}
\begin{tabular}{l*{3}{c}}
& A & B & C \\
\hline
1 & blah & blah & blah \\
2 & blah & blah & blah \\
3 & blah & blah & blah \\
\hline
\end{tabular}
\end{filecontents*}
\documentclass{beamer}
\usepackage{tikz}
\usetikzlibrary{calc}
\begin{document}
\begin{frame}
\begin{center}
\begin{tikzpicture}
\node (table) {\input{table.tex}};
\draw [red,ultra thick,rounded corners]
  ($(table.south west) !.3! (table.north west)$)
  rectangle 
  ($(table.south east) !.5! (table.north east)$);
\end{tikzpicture}
\end{center}
\end{frame}
\end{document}

Some explanation to the above code

There are several standard anchors on a node by default, denoted by compass directions, accessed with the syntax <node name>.<anchor>. For example will MyNode.north west be the top left corner of MyNode.

To get a coordinate between two existing coordinates you can use the TikZ library calc. This is described in section 13.5 Coordinate Calculations of the manual. It provides the syntax

($(<nodename or coordinate>) ! <factor> ! (<nodename or coordinate>)$)

Dollar signs indicate that a coordinate calculation should be done. The <factor> is a number saying how far, on the line between the two specified nodes, relative to the distance between the nodes, the point should be. For example,

($(0,0) !.3! (1,0)$)

is 30% of the way between (0,0) and (1,0), meaning (0.3,0).

In other words,

\draw [red,ultra thick,rounded corners]
  ($(table.south west) !.3! (table.north west)$)
  rectangle 
  ($(table.south east) !.5! (table.north east)$);

draws a rectangle from the point that is 30% of the distance from the lower left corner to the upper left corner, to the point that is halfway between the lower right and upper right corners.

Here's a sans-TikZ way of obtaining the rectangle via a coloured \fbox:

\documentclass{article}
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\newsavebox{\mytable}
\begin{document}

\begin{center}
\begin{lrbox}{\mytable}
\input{table.tex}
\end{lrbox}
%\setlength{\fboxrule}{2pt}% Modify rule width if necessary
\ooalign{%
  \hss\usebox{\mytable}\hss \cr
  {\color{red}%
   \fbox{\phantom{\rule[-5pt]{\dimexpr\wd\mytable+10pt}{\dimexpr\baselineskip+5pt}}}%
  }
}
\end{center}

\end{document}​

The table \input is stored in a box \mytable in order to obtain the width. The box is subsequently positioned with a 5pt overlap on either side of the table by setting a blank box of appropriate dimensions inside the coloured \fbox.

Within \ooalign, the table is centrred (since it's less wide than the 10pt-wider \fbox) using \hss...\hss. This is overprint with the coloured \fbox. Here is a quick course on \ooalign.

You could also reverse the sequence to use a shaded highlighting:

\documentclass{article}
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\newsavebox{\mytable}
\begin{document}

\begin{center}
\begin{lrbox}{\mytable}
\input{table.tex}
\end{lrbox}%
\setlength{\fboxrule}{2pt}% Modify rule width if necessary
\ooalign{%
  {\fcolorbox{red!50}{red!30}{%
     \phantom{\rule[-5pt]{\dimexpr\wd\mytable+10pt}{\dimexpr\baselineskip+5pt}}%
  }} \cr
  \hss\usebox{\mytable}\hss
}
\end{center}

\end{document}​

If you don't want to input the table into tikz, use this simple solution:

\begin{tikzpicture}[overlay]
\draw[red,ultra thick,rounded corners] (5.5,5.3) rectangle (6.4,9.2);
\end{tikzpicture}

Add this after the table if using overlays (e.g. \visible<>{}). Change the draw options and the coordinates manually. After a few iterations you will get it right.