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JoRussell-IDM / emod-parasite-genetics

A collection of development and example sims for commissioning DTK sims with explicit parasite genetics
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meeting with Jessica about FPG outputs as IBD inputs #19

Open JoRussell-IDM opened 3 years ago

JoRussell-IDM commented 3 years ago

Aim for comparable Garki scenario using Co-transmission model and FPG model with comparable analysis of genetic feature

JoRussell-IDM commented 3 years ago

https://github.com/jribado-IDM/tskit_test/blob/workflow-refactor/postparent/workflow/genepi_pairwise_ibs.py

unique_indices_df

linelist table of all unique infections in my population sample

https://github.com/jribado-IDM/tskit_test/blob/workflow-refactor/utilities/ibs-from-sites.py

give it a np array with 2000 different strains, returns list that has the hash of each 2000, then has subsequent functionality for the hash lookup in my sample back to a matrix against hash vs hash.

JoRussell-IDM commented 3 years ago

For collapse of simulated genome to sequenced observation: https://github.com/jribado-IDM/tskit_test/blob/workflow-refactor/postparent/workflow/genepi_to_genomicformat.py

Need parallel structure for identity : root : density

could use other parallel metadata to pre-filter the unique_genomes that enter into this whole pipeline

JoRussell-IDM commented 3 years ago

Working on this with sql_to_df.py in https://github.com/JoRussell-IDM/emod-parasite-genetics/tree/master/garki_long_run_genetic_behavior/analyzers

JoRussell-IDM commented 3 years ago

Plots of InsetChart