merged with master

.gitignore

@@ -1 +1,5 @@
+<<<<<<< HEAD
+=======
+# OS specific ignore file
+>>>>>>> master
 .DS_Store

pyrat-api-line-mutations-response.json

@@ -0,0 +1,32 @@
+[
+    {
+        "id": 3,
+        "name": "Mut-C",
+        "status": "active",
+        "possible_grades": [
+            {"id": 5, "name": "het"}, 
+            {"id": 6, "name": "hom"}, 
+            {"id": 7, "name": "wt"}
+        ]
+    },
+    {
+        "id": 1,
+        "name": "Mut-A",
+        "status": "active",
+        "possible_grades": [
+            {"id": 5, "name": "het"}, 
+            {"id": 6, "name": "hom"}, 
+            {"id": 7, "name": "wt"}
+        ]
+    },
+    {
+        "id": 2,
+        "name": "Mut-B",
+        "status": "inactive",
+        "possible_grades": [
+            {"id": 5, "name": "het"}, 
+            {"id": 6, "name": "hom"}, 
+            {"id": 7, "name": "wt"}
+        ]
+    }
+]

pyrat-api-lines-response-1.json

@@ -0,0 +1,10 @@
+[
+    {
+        "id": 1,
+        "name": "Line-A"
+    },
+    {
+        "id": 2,
+        "name": "Line-B"
+    }
+]

pyrat-api-lines-response-2.json

@@ -0,0 +1,6 @@
+[
+    {
+        "id": 3,
+        "name": "Line-C"
+    }
+]

pyrat-api-lines.csv

@@ -0,0 +1,4 @@
+id,name
+1,Line-A
+2,Line-B
+3,Line-C

pyrat-data-forbidden-genotypes.csv

@@ -9,7 +9,7 @@ ID-007,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ki/ki,,,
 ID-008,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ko/+,,,Mut-A,ko/-,Mut-B,het,,,Mut-A,-/ko,Mut-B,+/ko,,
 ID-009,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ki/+,,,Mut-A,ki/-,Mut-B,het,,,Mut-A,-/ki,Mut-B,+/ki,,
 ID-010,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ko/ko,,,Mut-A,ko/ko,Mut-B,het,,,Mut-A,wt,Mut-B,+,,
-ID-011,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,
+ID-011,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,,,,Mut-A,het,Mut-B,het,,,Mut-A,het,Mut-B,het,,
 ID-012,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,,Mut-B,,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,
 ID-013,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,,,,,,,,,,,,,,,,,,
 ID-014,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,,,,,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,

pyrat-data-forbidden-schemes.csv

@@ -0,0 +1,11 @@
+ID,Line / Strain (Name),DOB,Father,Mother,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father: Mutation 1,Father: Grade 1,Father: Mutation 2,Father: Grade 2,Father: Mutation 3,Father: Grade 3,Mother: Mutation 1,Mother: Grade 1,Mother: Mutation 2,Mother: Grade 2,Mother: Mutation 3,Mother: Grade 3
+ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,hom,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
+ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,hom,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
+ID-003,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
+ID-004,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
+ID-005,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
+ID-006,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-B,hom,Mut-A,het,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
+ID-007,Line-AB,02/01/2025,ID-F2,ID-M2,End of experiment,Mut-B,hom,Mut-A,het,,,Mut-A,hom,Mut-B,het,,,Mut-A,het,Mut-B,hom,,
+ID-008,Line-AB,02/01/2025,ID-F2,ID-M2,End of experiment,Mut-B,wt,Mut-A,wt,,,Mut-A,hom,Mut-B,het,,,Mut-A,het,Mut-B,hom,,
+ID-009,Line-DE,06/06/2025,ID-F13,ID-M13,End of experiment,Mut-D,hom,Mut-E,hom,,,Mut-D,het,,,,,Mut-E,het,,,,
+ID-010,Line-DE,06/06/2025,ID-F13,ID-M13,End of experiment,Mut-D,hom,Mut-E,hom,,,Mut-D,het,,,,,Mut-E,het,,,,

standardised-data-forbidden-genotypes.csv

@@ -4,7 +4,7 @@ ID-006,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_hom,ho
 ID-007,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_hom,hom_het,wt_hom
 ID-008,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_het,het_het,het_het
 ID-009,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_het,het_het,het_het
-ID-011,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_wt,hom_het,wt_hom
+ID-011,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_wt,het_het,het_het
 ID-012,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,,hom_het,wt_hom
 ID-013,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,,wt_wt,wt_wt
 ID-014,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,,hom_het,wt_hom

standardised-data-forbidden-schemes.csv

@@ -0,0 +1,8 @@
+ID_offspring,line_name,date_of_birth,ID_father,ID_mother,sacrifice_reason,n_mutations,mutations,genotype_offspring,genotype_father,genotype_mother
+ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,hom_hom,het_hom,hom_het
+ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,hom_hom,het_hom,hom_het
+ID-003,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_hom,het_hom,hom_het
+ID-004,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_hom,het_hom,hom_het
+ID-005,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_hom,het_hom,hom_het
+ID-006,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,2,Mut-A_Mut-B,het_hom,het_hom,hom_het
+ID-007,Line-AB,02/01/2025,ID-F2,ID-M2,End of experiment,2,Mut-A_Mut-B,het_hom,hom_het,het_hom