Question on files

Hi,
I am using PHP to make a website related to biology. In this site I use PHP code to communicate with external programms (not in PHP, but some biological packages). These programms write their output in temporary files, which I then read using fread() or file_get_contents() functions.
My problem is that these functions seem to have a restriction as to the size of the file that they can read. Is there any other way I read big files (for files close to 20-30MBs for example)?
Please note that there is no other way for me to do this because these programs, by default, write their output to a text file, so I can't use PHP's system commands and read the output on the fly. The output file is first created and then I read it into a string and parse it according to what I need.