parse geno input data

1 files changed, 44 insertions, 1 deletions

diff --git a/wqflask/wqflask/ctl/gn3_ctl_analysis.py b/wqflask/wqflask/ctl/gn3_ctl_analysis.py
index 2b5c0f0b..9ee85d3d 100644
--- a/wqflask/wqflask/ctl/gn3_ctl_analysis.py
+++ b/wqflask/wqflask/ctl/gn3_ctl_analysis.py
@@ -1,8 +1,45 @@
 import requests
-
+from dataclasses import dataclass
 from utility.tools import GN3_LOCAL_URL
 
 
+@dataclass
+class CtlDatabase:
+    """class for keeping track of ctl db data"""
+
+    dataset: dict
+
+    trait_db_list: list
+
+
+def parse_geno_data(dataset_group_name) ->dict:
+	"""function to parse geno file data"""
+	genofile_location = locate(dataset.group.name + ".geno", "genotype")
+	parser = genofile_parser.ConvertGenoFile(genofilelocation)
+
+	parser.process_csv()
+
+	# get marker and marker names
+
+    markers = []
+    markernames = []
+    for marker in parser.markers:
+        markernames.append(marker["name"])
+        markers.append(marker["genotypes"])
+
+    return {
+
+    "genotypes":list(itertools.chain(*markers)),
+    "markernames":markernames
+    "individuals":parser.individuals,
+
+
+    }
+
+
+
+
+
 def parse_form_data(form_data: dict):
     """function to parse/validate form data
     input: dict containing required data
@@ -10,6 +47,10 @@ def parse_form_data(form_data: dict):
 
     """
 
+    trait_db_list = [trait.strip()
+                          for trait in requestform['trait_list'].split(',')]
+    form_data["trait_db_list"] = [x for x in  trait_db_list if x]
+
     form_data["nperm"] = int(form_data["nperm"])
     form_data["significance"] = float(int(form_data["significance"]))
     form_data["strategy"] = form_data["strategy"].capitalize()
@@ -21,6 +62,8 @@ def run_ctl():
     """function to make an api call
     to gn3 and run ctl"""
 
+    CtlObj = CtlDatabase()
+
     ctl_api = f"{GN3_LOCAL_URL}/api/wgcna/run_wgcna"
 
     response = requests.post(ctl_api, json={