Test out generation of traits file

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* As part of the development effort, this commit provides a proof-of-concept
  as a reference for generating the traits data file.

  It might be useful for verifying that the functions that are called are
  working as is expected.

1 files changed, 67 insertions, 0 deletions

diff --git a/qtlfilesexport.py b/qtlfilesexport.py
new file mode 100644
index 0000000..2e7c9c2
--- /dev/null
+++ b/qtlfilesexport.py
@@ -0,0 +1,67 @@
+"""
+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
+"""
+import random
+import string
+from gn3.computations.slink import slink
+from gn3.db_utils import database_connector
+from gn3.computations.heatmap import export_trait_data
+from gn3.db.traits import retrieve_trait_data, retrieve_trait_info
+from gn3.computations.heatmap import (
+    cluster_traits,
+    compute_heatmap_order,
+    generate_traits_file,
+    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 random_string(length):
+    return "".join(
+        random.choices(
+            string.ascii_letters + string.digits, k=length))
+
+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]
+    strains = list(set([k for td in traits_data_list for k in td["data"].keys()]))
+    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]
+    strains_values2 = strains_and_values[1][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))
+
+if __name__ == "__main__":
+    main()