diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/qtlreaper.py | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 9b20309..8c0e6de 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -86,6 +86,31 @@ def run_reaper( subprocess.run(command_list, check=True) return (output_filename, permu_output_filename) +def organise_reaper_main_results(parsed_results): + def __organise_by_chromosome(chr_name, items): + chr_items = [item for item in items if item["Chr"] == chr_name] + return { + "Chr": str(chr_name), + "loci": [{ + "Locus": locus["Locus"], + "cM": locus["cM"], + "Mb": locus["Mb"], + "LRS": locus["LRS"], + "Additive": locus["Additive"], + "pValue": locus["pValue"] + } for locus in chr_items]} + + def __organise_by_id(identifier, items): + id_items = [item for item in items if item["ID"] == identifier] + unique_chromosomes = {item["Chr"] for item in id_items} + return { + "ID": identifier, + "chromosomes": [ + __organise_by_chromosome(chromo, id_items) + for chromo in sorted(unique_chromosomes)]} + + unique_ids = {res["ID"] for res in parsed_results} + return [__organise_by_id(_id, parsed_results) for _id in sorted(unique_ids)] def parse_reaper_main_results(results_file): """ |