diff options
| -rw-r--r-- | gn3/computations/heatmap.py | 42 | ||||
| -rw-r--r-- | gn3/db/traits.py | 5 |
2 files changed, 27 insertions, 20 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py index e0ff05b..92014cf 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/computations/heatmap.py @@ -6,8 +6,12 @@ generate various kinds of heatmaps. from functools import reduce from typing import Any, Dict, Sequence from gn3.computations.slink import slink -from gn3.db.traits import retrieve_trait_data, retrieve_trait_info from gn3.computations.correlations2 import compute_correlation +from gn3.db.genotypes import build_genotype_file, load_genotype_samples +from gn3.db.traits import ( + retrieve_trait_data, + retrieve_trait_info, + generate_traits_filename) def export_trait_data( trait_data: dict, strainlist: Sequence[str], dtype: str = "val", @@ -125,7 +129,7 @@ def cluster_traits(traits_data_list: Sequence[Dict]): return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list)) -def heatmap_data(formd, search_result, conn: Any): +def heatmap_data(traits_names, conn: Any): """ heatmap function @@ -142,39 +146,37 @@ def heatmap_data(formd, search_result, conn: Any): TODO: Elaborate on the parameters here... """ threshold = 0 # webqtlConfig.PUBLICTHRESH - cluster_checked = formd.formdata.getvalue("clusterCheck", "") - strainlist = [ - strain for strain in formd.strainlist if strain not in formd.parlist] - genotype = formd.genotype - def __retrieve_traitlist_and_datalist(threshold, fullname): trait = retrieve_trait_info(threshold, fullname, conn) return (trait, retrieve_trait_data(trait, conn)) traits_details = [ __retrieve_traitlist_and_datalist(threshold, fullname) - for fullname in search_result] + for fullname in traits_names] traits_list = tuple(x[0] for x in traits_details) traits_data_list = [x[1] for x in traits_details] exported_traits_data_list = tuple( export_trait_data(td, strainlist) for td in traits_data_list) + genotype_filename = build_genotype_file(traits_list[0]["riset"]) + strainlist = load_genotype_samples(genotype_filename) + slink_data = slink(cluster_traits(exported_traits_data_list)) + ordering_data = compute_heatmap_order(slink_data) + strains_and_values = retrieve_strains_and_values( + orders, strainlist, exported_traits_data_list) + strains_values = strains_and_values[0][1] + trait_values = [t[2] for t in strains_and_values] + traits_filename = generate_traits_filename() + generate_traits_file(strains_values, trait_values, traits_filename) return { - "target_description_checked": formd.formdata.getvalue( - "targetDescriptionCheck", ""), - "cluster_checked": cluster_checked, - "slink_data": ( - slink(cluster_traits(exported_traits_data_list)) - if cluster_checked else False), - "sessionfile": formd.formdata.getvalue("session"), - "genotype": genotype, - "nLoci": sum(map(len, genotype)), + "slink_data": slink_data, + "ordering_data": ordering_data, "strainlist": strainlist, - "ppolar": formd.ppolar, - "mpolar":formd.mpolar, + "genotype_filename": genotype_filename, "traits_list": traits_list, "traits_data_list": traits_data_list, - "exported_traits_data_list": exported_traits_data_list + "exported_traits_data_list": exported_traits_data_list, + "traits_filename": traits_filename } def compute_heatmap_order( diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 1031e44..ccb101a 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,4 +1,5 @@ """This class contains functions relating to trait data manipulation""" +from gn3.settings import TMPDIR from typing import Any, Dict, Union, Sequence from gn3.function_helpers import compose from gn3.db.datasets import retrieve_trait_dataset @@ -666,3 +667,7 @@ def retrieve_trait_data(trait: dict, conn: Any, strainlist: Sequence[str] = tupl {k:v for k, v in x.items() if x != "strain_name"}), data))} return {} + +def generate_traits_filename(base_path: str = TMPDIR): + return "{}/traits_test_file_{}.txt".format( + os.path.abspath(base_path), random_string(10)) |