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