Implements Gemma output to Result_table workflow

lib/gemma.ml

@@ -31,6 +31,13 @@ let%pworkflow phenotype_of_tree nhx =
 let template_of_lmm lmm =
   int (match lmm with `Wald -> 1 | `LRT -> 2 | `Score -> 3 | `All -> 4)
 
+class type univariate_lmm_output =
+  object
+    inherit tsv
+
+    method format : [ `gemma_test_output ]
+  end
+
 let univariate_lmm ~lmm ~genotype ~phenotype ~relatedness_matrix =
   Workflow.shell ~descr:"gemma.univariate_lmm"
     [
@@ -63,3 +70,15 @@ let calculate_relatedness_matrix ~mode ~genotype ~phenotype =
         ];
       cmd "cp" [ tmp // relatedness_filename mode; dest ];
     ]
+
+let%pworkflow[@version 3] result_table_of_output gemma_output =
+  let module R = Reviewphiltrans_toolbox.Gemma.Result_file in
+  let open Phylogenetics in
+  match R.of_file [%path gemma_output] with
+  | Error msg -> failwith msg
+  | Ok result_file ->
+      R.to_result_table result_file ~site_aggregator:(fun items ->
+          List1.to_list items
+          |> List.map ~f:R.min_pval_of_item
+          |> List.reduce_exn ~f:Float.min)
+      |> Reviewphiltrans_toolbox.Result_table.to_file ~output:[%dest]

lib/gemma.mli

@@ -18,10 +18,20 @@ val calculate_relatedness_matrix :
   phenotype:bimbam file ->
   relatedness_matrix file
 
+class type univariate_lmm_output =
+  object
+    inherit tsv
+
+    method format : [ `gemma_test_output ]
+  end
+
 val univariate_lmm :
   lmm:[ `Wald | `LRT | `Score | `All ] ->
   genotype:bimbam file ->
   phenotype:bimbam file ->
   relatedness_matrix:relatedness_matrix file ->
-  text file
+  univariate_lmm_output file
 
+val result_table_of_output : 
+  univariate_lmm_output file ->
+  text file
\ No newline at end of file