pyani.scripts.delta_filter_wrapper module¶
Wrapper for MUMmer 3.23 delta-filter script.
It is required in order to catch STDOUT ahead of the SGE job runner so that pyani can run on SGE/OGE scheduling systems.
The wrapper does not modify the output of delta-filter, and is called in exactly the same way, passing arguments through directly. The only departure from this is that the first argument is the path to delta-filter, and the final argument denotes the output filtered delta file path, so that redirection (which no longer works with SGE/OGE) is not necessary.
For example, the delta-filter command
delta-filter [options] <delta file> > <filtered delta file>
becomes
delta_filter_wrapper.py delta-filter [options] <delta file> <filtered delta file>
This wrapper is not very robust, but will be improved in later versions of pyani.