Source codeΒΆ

The source code is naturally available in the gzipped tar-archive since the Python scripts are uncompiled and the accessory file, ‘’, 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 ‘’ 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

        filename    filename of blastclust output
        sequenceIDs list of sequence IDs with unique identifiers
                    right after the '>' symbol
        PathError   raised if the file does not exists
        ValueError  rasied if no unique identifiers could be found
                    and removed

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