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+"""
+Test the qtlfiles export of traits files
+
+Run with:
+
+ env SQL_URI="mysql://<user>:<password>@<host>:<port>/db_webqtl" python3 qtlfilesexport.py
+
+replacing the variables in the angled brackets with the appropriate values
+"""
+from gn3.computations.slink import slink
+from gn3.db_utils import database_connector
+from gn3.computations.qtlreaper import run_reaper
+from gn3.computations.heatmap import export_trait_data
+from gn3.db.traits import retrieve_trait_data, retrieve_trait_info
+from gn3.db.genotypes import build_genotype_file, load_genotype_samples
+from gn3.computations.qtlreaper import random_string, generate_traits_file
+from gn3.computations.heatmap import (
+ cluster_traits,
+ compute_heatmap_order,
+ retrieve_strains_and_values)
+
+TMPDIR = "tmp/qtltests"
+
+def trait_fullnames():
+ """Return sample names for traits"""
+ return [
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM2260338",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM3140576",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM5670577",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM2070121",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM103990541",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM1190722",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM6590722",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064",
+ "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"]
+
+def main():
+ """entrypoint function"""
+ conn = database_connector()[0]
+ threshold = 0
+ traits = [
+ retrieve_trait_info(threshold, fullname, conn)
+ for fullname in trait_fullnames()]
+ traits_data_list = [retrieve_trait_data(t, conn) for t in traits]
+ genotype_filename = build_genotype_file(traits[0]["riset"])
+ strains = load_genotype_samples(genotype_filename)
+ exported_traits_data_list = [
+ export_trait_data(td, strains) for td in traits_data_list]
+ slinked = slink(cluster_traits(exported_traits_data_list))
+ orders = compute_heatmap_order(slinked)
+ strains_and_values = retrieve_strains_and_values(
+ orders, strains, exported_traits_data_list)
+ strains_values = strains_and_values[0][1]
+ trait_values = [t[2] for t in strains_and_values]
+ traits_filename = "{}/traits_test_file_{}.txt".format(
+ TMPDIR, random_string(10))
+ generate_traits_file(strains_values, trait_values, traits_filename)
+ print("Generated file: {}".format(traits_filename))
+
+ main_output, permutations_output = run_reaper(
+ genotype_filename, traits_filename, separate_nperm_output=True)
+
+ print("Main output: {}, Permutation output: {}".format(
+ main_output, permutations_output))
+
+if __name__ == "__main__":
+ main()