Gemma pipeline for relatedness matrix

lib/gemma.ml

+open Core_kernel
+open Bistro
+open Bistro.Shell_dsl
+
+class type relatedness_matrix = object
+  inherit text
+  method format : [`gemma_relatedness_matrix]
+end
+
+let%pworkflow genotype_of_fasta fasta =
+  let module G = Reviewphiltrans_toolbox.Gemma in
+  G.write_genotypes ~alignment:[%path fasta] ~output:[%dest]
+
+let template_of_mode m =
+  int (
+    match m with
+    | `Centered -> 1
+    | `Standardized -> 2
+  )
+
+let calculate_relatedness_matrix ~mode ~genotype ~phenotype =
+  Workflow.shell ~descr:"gemma.calculate_relatedness_matrix" [
+    cmd "gemma" [
+      opt "-g" dep genotype ;
+      opt "-p" dep phenotype ;
+      opt "-gk" template_of_mode mode ;
+      opt "-o" Fn.id dest ;
+    ]
+  ]
\ No newline at end of file

lib/gemma.mli

+open Bistro
+open File_formats
+
+class type relatedness_matrix = object
+  inherit text
+  method format : [`gemma_relatedness_matrix]
+end
+
+val genotype_of_fasta : aminoacid_fasta file -> bimbam file
+
+val calculate_relatedness_matrix :
+  mode:[`Centered | `Standardized] ->
+  genotype:bimbam file ->
+  phenotype:bimbam file ->
+  relatedness_matrix file