changes to simplify and de-duplicate output

pyrat-data-forbidden-genotypes-false.csv

@@ -1,15 +0,0 @@
-ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
-ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,
-ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,
-ID-003,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,Tg,Mut-B,Tg,,,Mut-A,T,Mut-B,-,,,Mut-A,T,Mut-B,-,,
-ID-004,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,-,Mut-B,-,,,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,
-ID-005,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,+,Mut-B,-,,,Mut-A,-,Mut-B,-,,
-ID-006,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,ko/ko,,
-ID-007,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ki/ki,,,Mut-A,ki/ki,Mut-B,het,,,Mut-A,wt,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,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-genotypes-true.csv

@@ -1,15 +0,0 @@
-ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
-ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,
-ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,
-ID-003,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,Tg,Mut-B,Tg,,,Mut-A,T,Mut-B,-,,,Mut-A,T,Mut-B,-,,
-ID-004,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,-,Mut-B,-,,,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,
-ID-005,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,+,Mut-B,-,,,Mut-A,-,Mut-B,-,,
-ID-006,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,ko/ko,,
-ID-007,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ki/ki,,,Mut-A,ki/ki,Mut-B,het,,,Mut-A,wt,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,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-genotypes.csv

@@ -2,15 +2,15 @@ ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,
 ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,
 ID-003,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,Tg,Mut-B,Tg,,,Mut-A,T,Mut-B,-,,,Mut-A,T,Mut-B,-,,
-ID-004,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,+,Mut-B,-,,,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,
-ID-005,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,
+ID-004,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,+,Mut-B,-,,,Mut-A,het,Mut-B,het,,,Mut-A,het,Mut-B,het,,
+ID-005,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,het,,,Mut-A,+,Mut-B,+,,,Mut-A,-,Mut-B,-,,
 ID-006,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,ko/ko,,
 ID-007,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,ki/ki,,,Mut-A,ki/ki,Mut-B,het,,,Mut-A,wt,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-010,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,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,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,,
-ID-015,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,dp1Tyb,Mut-B,hom,,,Mut-A,hom,Mut-B,dp1Tyb,,,Mut-A,wt,Mut-B,hom,,
+ID-015,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,dp1tyb,Mut-B,hom,,,Mut-A,hom,Mut-B,dp1tyb,,,Mut-A,wt,Mut-B,hom,,

standardised-data-forbidden-genotypes-false.csv

@@ -1,13 +0,0 @@
-ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,mutation_2,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,het_hom,hom_het,wt_hom
-ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,wt_hom,wt_hom,wt_hom
-ID-004,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,hom_hom,het_hom,het_hom
-ID-005,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,wt_hom,hom_hom
-ID-006,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,hom_het,wt_hom
-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,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-genotypes-true.csv

@@ -1,12 +0,0 @@
-ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,mutation_2,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,het_hom,hom_het,wt_hom
-ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,hom_wt,hom_wt,hom_wt
-ID-006,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,hom_het,wt_hom
-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-010,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,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