alistats mode: computation of mean number of residues per column

app/reviewphiltrans_app.ml

@@ -6,5 +6,6 @@ let () =
     "simulation", Pipeline.simulation_command ;
     "detection",  Pipeline.detection_command ;
     "validation", Pipeline.validation_command ;
+    "alistats", Alistats.command ;
   ]
   |> Command.run

lib/alignment.ml

@@ -8,9 +8,11 @@ type t = {
   seqs : string array ;
 }
 
+let fmt = Biocaml_ez.Fasta.{ default_fmt with allow_empty_lines = true }
+
 let from_fasta fn =
   match
-    Biocaml_ez.Fasta.with_file fn ~f:(fun _ items ->
+    Biocaml_ez.Fasta.with_file ~fmt fn ~f:(fun _ items ->
         Stream.map items ~f:(fun i -> i.description, i.sequence)
         |> Stream.to_array
         |> Array.unzip

lib/alistats.ml

+open Core
+
+let main ~alignment () =
+  match Alignment.from_fasta alignment with
+  | Ok al ->
+    let mu, sigma = Alignment.number_of_residues_per_column_stats al in
+    printf "%f %f\n" mu sigma
+  | Error (`Msg msg) -> failwith msg
+
+let command =
+  let open Command.Let_syntax in
+  Command.basic
+    ~summary:"Computes stats on alignments"
+    [%map_open
+      let alignment =
+        flag "--alignment" (required string) ~doc:"PATH Output directory"
+      in
+      main ~alignment
+    ]