Since you are writing your output line by line, you don't need to store a matrix. You need a hash which maintains the number of times the word is found in a given paragraph. Therefore,

• open the output file
• write the key line as an ordered set (array) with tab (\t) characters in appropriate places
• make a hash of all 100 keys with zero as the value
• then, for each paragraph,
  
  1. read from input file into a string until you find '-100'
  2. see if each character group (until space, newline, or punctuation) is a key
  3. if so, increment the hash value of that key. If not, ignore
  4. write out the values to the output file as an ordered set
  5. reset the hash values to zero
• close the files

You'll want to deal with capitalization somehow, as well. :D