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bioa.algorithms.reconstruction.min_unsplittable_flows_resolution

min_unsplittable_flows_resolution(graph, flow_num, nthreads=0, timeout=300, threshold=1e-05)[source]

Min-k unsplittable flows method. This tries to find k paths in the graph that cover the reads with minimum amount of flow.

Parameters :

graph : DecliquedAmpliconReadGraph

Amplicon read graph with fork vertices added.

flow_num : int

The number of paths to try.

nthreads : int, optional default=0

The number of threads to use. 0 = Use maximum number of threads (i.e. CPUs) 1 = Single Threaded n = Use n threads

timeout : int, optional default=300

The number of seconds to run cplex until timeout.

threshold : float, optional default=1e-5

The threshold for determining a variable being selected or not.

Returns :

quasispecies : dict

Quasispecies spectrum with sequences as keys and frequency as value.

Notes

Requires CPLEX and CPLEX Python module to be installed. http://www.cplex.com