Source code
===========
The source code is naturally available in the gzipped tar-archive since the 
Python scripts are uncompiled and the accessory file, 'fluff.py', that 
contains a host of functions important for the operation of the pipeline, is
supplied in the uncompiled state. Upon the first run of the pipeline, this 
file will compile into a byte-compiled version to improve loading times. 

Nevertheless the entire source code is available to the user for inspection 
and correction of bugs. The code should be fairly well commented and each 
function in 'fluff.py' has a docstring explaining what it does, what it 
requires as input, what output it gives and also what errors it might produce.
It can be accessed by importing it and calling their respective doc-method, 
example::
    >>> import fluff
    >>> print fluff.parse_blastclust.__doc__
    
        Parses blastclust output into a nested list structure
        
        Input:
            filename    filename of blastclust output
        Output:
            sequenceIDs list of sequence IDs with unique identifiers
                        right after the '>' symbol
        Errors:
            PathError   raised if the file does not exists
            ValueError  rasied if no unique identifiers could be found 
                        and removed