- bpm.bpmreader: Provides a function to read and parse a BPM file into a nice data structure.
- bpm.cmdargs
- bpm.debug
- bpm.enrichment: enrichment.py provides functions for gathering, reading, writing and sorting
GO enrichment information from Funcassociate.
- bpm.faclient: A client class for the FuncAssociate web service at
- bpm.faread: 'faread.py' is a wrapper around 'faclient.py' that handles the nastiness of
the data we get back.
- bpm.geneinter: 'geneint.py' is the module that processes the genetic interaction input file.
- bpm.parallel: 'parallel.py' is a set of functions that make parallelizing functions much
easier. Namely, a 'pmap' function that will use the single-threaded version if
parallelization isn't available.
- bpm.partition: 'partition.py' is a module that parallelizes the process of partitioning random
sets of genes. This is where most of the complexity of Genecentric is,
particularly in the 'localmaxcut' function.
- bpm.prune: 'prune.py' provides all the functions required to prune a set of BPMs after
they have been generated.
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