10X-deconvolve

Trying to deconvolve single tag assignment for multiple molecules

Scripts

For the majority of the scripts, argparse is used. To know how to use it please use the -h option.

Data simulation

• generate_fake_molecule_graph.py: Create a linear molecule graph, where the molecules are linked to the d molecules on their left and d molecules on their right.

• generate_fake_barcode_graph.py: Take a barcode graph as input (gexf formated) and outputs a barcode graph. The barcode graph is create by fusion of nodes from the molecule graph.

Data structures and algorithms

• to_d2_graph.py: Mount a barcode graph into memory and create a d2 graph from it.

• evaluate.py: take a d2 graph gexf file and and analyse it. Look for an approximation of the longest correct path to reconstruct a molecule graph. Take as input a d2 graph where the truth is known in the node names (the format used to create fake data).

• analyse_d2_tsv.py: Take an tsv optimization file of a d2 graph and look for the variables coverage. Outputs the missing variables (if exists).

Run the tests

export PYTHONPATH=deconvolution/
pytest tests
export PYTHONPATH=