University Information Technology Services
Research and Academic Computing 


GeneIndex





 




Usage: geneindex [-p | -f] [-v visualMode] [-w word] [-i wordFile] 
[-o outputFile] wordLength [sequenceFile]

  -f: Output frequency information only. 
  -p: Output position information only.
      if none is set, the default is to output all information.
  -v: Visualize data using Tcl/Tk. Four options:
      p: Visualize frequency information in the order of word (P)ositions.
      a: Visualize frequency information in the (A)lphabet order of words.
      o: Visualize frequency information in descending (O)rder.
      d: Visualize (D)istribution of all words' occurance.
  -w: Give a particular word and retrieve its frequency and positions.
  -i: List words in wordFile and retrieve their frequencies and positions.
      CANNOT specify both -w and -i.
  -o: Output data to outputFile. The default is the standard output.
  WordLength is required. If no dnaFile given, the default is the standard input.

For example: 


      geneindex -f -v d -w acgt -o myResult 4 mySequence 

  This command will get the information of the word 'acgt' in the 
  sequence file mySequence, and output its frequency to the file
  named myResult. Meanwhile, view position information using Tcl/Tk.