Alistats: added convergent/ancestral differentiated GC computation

.ocamlinit

@@ -4,7 +4,7 @@ open Pipeline2
 module Dbg = Reviewphiltrans.Debug
 
 let auc ?mode d =
-  let a = 
+  let a =
     result_table ?mode d
     |> Convergence_detection.recall_precision_auc_table
     |> Dbg.eval
@@ -13,6 +13,11 @@ let auc ?mode d =
 let gc_contents ?pos d =
   d |> nucleotide_alignment |> Dbg.path |> Alistats.nucleotide_fasta_gc ?pos
 
+let ac_gc_stats ?pos d =
+  let al = d |> nucleotide_alignment |> Dbg.path in
+  let tree = tree d |> Dbg.path in
+  Alistats.nucleotide_fasta_gc_ac ?pos tree al
+
 let count_py w =
   Sys.command (Core.sprintf "python lib/scripts/count_detected.py %s" (Dbg.path w))
   |> ignore

lib/alistats.ml

@@ -21,14 +21,13 @@ type gc_stat = {
   gc_variance_among_sequences : float ;
 }
 
-let nucleotide_fasta_gc ?pos fa =
+let seq_gc ?pos seqs =
   let pos = Option.map pos ~f:(function
       | `first -> 0
       | `second -> 1
       | `third -> 2
     )
   in
-  let seqs = strings_from_fasta fa in
   let gc_counts = Array.map seqs ~f:(fun seq ->
       let len = if pos <> None then String.length seq / 3 else String.length seq in
       let sum = String.foldi ~init:0 ~f:(fun i a c -> a + if is_gc ?pos i c then 1 else 0) seq in
@@ -41,6 +40,22 @@ let nucleotide_fasta_gc ?pos fa =
   let gc_mean = Array.fold gc_counts ~init:0. ~f:(fun acc (_, k) -> acc +. k /. total_len) in
   { gc_mean ; gc_variance_among_sequences }
 
+let nucleotide_fasta_gc ?pos fa =
+  let seqs = strings_from_fasta fa in
+  seq_gc ?pos seqs
+
+let nucleotide_fasta_gc_ac ?pos tree fa =
+  let tree = Convdet.Simulator.tree_from_file tree in
+  let seqs = strings_from_fasta fa in
+  let leaf_state =
+    Phylogenetics.Tree.map_leaves tree ~root:(0., 0) ~f:(fun _ b -> snd b = 0)
+    |> Array.of_list
+  in
+  let ancestral_seqs, convergent_seqs =
+    Array.partitioni_tf seqs ~f:(fun i _ -> leaf_state.(i))
+  in
+  seq_gc ?pos ancestral_seqs, seq_gc ?pos convergent_seqs
+
 let main ~alignment () =
   match Alignment.from_fasta alignment with
   | Ok al ->