a few systematic/reproducible tests

.gitignore

@@ -0,0 +1,4 @@
+PhyloCSF.Linux.x86_64
+PhyloCSF.Darwin.x86_64
+_build
+*.native

Makefile

@@ -11,7 +11,11 @@ PhyloCSF: CamlPaml
 
 CamlPaml:
 	$(MAKE) -C lib/CamlPaml $(MFLAGS) reinstall
-	
+
+test: PhyloCSF
+	$(MAKE) -C lib/CamlPaml $(MFLAGS) test
+	$(MAKE) -C src $(MFLAGS) test
+
 clean:
 	$(MAKE) -C lib/CamlPaml clean
 	$(MAKE) -C src clean

src/Makefile

@@ -1,8 +1,9 @@
 all:
 	ocamlbuild PhyloCSF.native
 
-test:
-	ocamlbuild testSim.native
+test: all
+	ocamlbuild testSim.native test.native
+	./test.native -verbose
 
 clean:
 	rm -f *~

src/_tags

@@ -1,3 +1,4 @@
 <**/*.ml> or <**/*.mli>: pp(ocaml+twt)
+<test.ml> or <test.native>: pkg_should, pkg_oUnit, pkg_str
 true: debug, pkg_batteries, pkg_CamlPaml
 

src/test.ml

@@ -0,0 +1,96 @@
+open Batteries
+open Printf
+open OUnit
+open Should
+
+let dn_here = Filename.dirname Sys.argv.(0)
+
+let fn_PhyloCSF = Filename.concat dn_here "PhyloCSF.native"
+
+(* test results on the three bundled example alignments *)
+
+let run_PhyloCSF species params =
+  let cmd = sprintf "%s %s %s" fn_PhyloCSF (Filename.concat dn_here ("../PhyloCSF_Parameters/" ^ species)) params
+
+  let phylocsf_in = Unix.open_process_in ~cleanup:true cmd
+
+  let phylocsf_answer = input_line phylocsf_in
+  match Unix.close_process_in phylocsf_in with
+    | Unix.WEXITED 0 -> String.nsplit phylocsf_answer "\t"
+    | _ -> raise Exit
+
+let talAA () =
+  let ans = run_PhyloCSF "12flies" "../PhyloCSF_Examples/tal-AA.fa"
+  print_endline (String.join "\t" ans)
+  List.nth ans 1 $hould # equal "score(decibans)"
+  float_of_string (List.nth ans 2) $hould # be # within (297.62,297.63)
+
+let aldh2_ex5_out () =
+  let ans = run_PhyloCSF "29mammals" "../PhyloCSF_Examples/ALDH2.exon5.fa"
+  print_endline (String.join "\t" ans)
+  List.nth ans 1 $hould # equal "score(decibans)"
+  float_of_string (List.nth ans 2) $hould # be # within (-178.93,-178.92)
+
+let aldh2_ex5_in () =
+  let ans = run_PhyloCSF "29mammals" "../PhyloCSF_Examples/ALDH2.exon5.fa --frames=6"
+  print_endline (String.join "\t" ans)
+  List.nth ans 1 $hould # equal "max_score(decibans)"
+  float_of_string (List.nth ans 2) $hould # be # within (218.26,218.27)
+  int_of_string (List.nth ans 3) $hould # equal 1
+  int_of_string (List.nth ans 4) $hould # equal 111
+  List.nth ans 5 $hould # equal "+"
+
+let aldh2_mRNA () =
+  let ans = run_PhyloCSF "29mammals" "../PhyloCSF_Examples/Aldh2.mRNA.fa --orf=ATGStop --frames=3 --removeRefGaps --aa"
+  print_endline (String.join "\t" ans)
+  List.nth ans 1 $hould # equal "max_score(decibans)"
+  float_of_string (List.nth ans 2) $hould # be # within (2013.92,2013.93)
+  int_of_string (List.nth ans 3) $hould # equal 343
+  int_of_string (List.nth ans 4) $hould # equal 1899
+  string (List.nth ans 5) $hould # be # matching (Str.regexp "^MLRAALTTVRRGPRLSRLLSAAA.*")
+
+let example_tests = "examples" >::: [
+    "tal-AA" >:: talAA;
+    "ALDH2 ex5 out-of-frame" >:: aldh2_ex5_out;
+    "ALDH2 ex5 in-frame" >:: aldh2_ex5_in;
+    "Aldh2 mRNA" >:: aldh2_mRNA
+  ]
+
+(* simulations
+   FIXME: currently there is no verification of the results except that PhyloCSF
+          successfully exits; you have to eyeball the test stdout. *)
+
+let fn_testSim = Filename.concat dn_here "testSim.native"
+
+let check cmd = match Sys.command cmd with
+  | 0 -> ()
+  | c when (c=130 || c=255) -> exit c (* ctrl-C *)
+  | c -> failwith (sprintf "Child process exit code %d" c)
+
+let sim_AsIs_fixed () =
+  check (sprintf "%s --maxUTR=0 --constantFrame --constantStrand 12flies ' --strategy=fixed'" fn_testSim)
+
+let sim_AsIs_mle () =
+  check (sprintf "%s --maxUTR=0 --constantFrame --constantStrand 12flies ' --strategy=mle'" fn_testSim)
+
+let sim_ATGStop_fixed () =
+  check (sprintf "%s 12flies ' --orf=ATGStop --frames=6 --strategy=fixed'" fn_testSim)
+
+let sim_ATGStop_mle () =
+  check (sprintf "%s 12flies ' --orf=ATGStop --frames=6 --strategy=mle'" fn_testSim)
+
+
+let sim_tests = "simulations" >::: [
+    "AsIs_fixed" >:: sim_AsIs_fixed;
+    "AsIs_mle" >:: sim_AsIs_mle;
+    "ATGStop_fixed" >:: sim_ATGStop_fixed;
+    "ATGStop_mle" >:: sim_ATGStop_mle
+  ]
+
+let all_tests =
+    "PhyloCSF" >::: [
+      sim_tests;
+      example_tests
+    ]
+
+run_test_tt_main all_tests

src/testSim.ml

@@ -16,7 +16,7 @@ module Codon = CamlPaml.Code.Codon64
 let opt_parser = OptParser.make ~usage:"%prog 12flies \" --frames=6 --orf=ATGStop --strategy=fixed\"" ()
 let opt ?group ?h ?hide ?s ?short_names ?l ?long_names x = OptParser.add opt_parser ?group ?help:h ?hide ?short_name:s ?long_name:l x; x
 
-let n = opt ~s:'n' (StdOpt.int_option ~default:8 ())
+let n = opt ~s:'n' (StdOpt.int_option ~default:5 ())
 let min_utr = opt ~l:"minUTR" (StdOpt.int_option ~default:10 ())
 let max_utr = opt ~l:"maxUTR" (StdOpt.int_option ~default:50 ())
 let min_cds = opt ~l:"minCDS" (StdOpt.int_option ~default:40 ())
@@ -138,6 +138,7 @@ let run_phylocsf aln =
 	let phylocsf_answer = input_line phylocsf_in
 	match Unix.close_process (phylocsf_in,phylocsf_out) with
 		| Unix.WEXITED 0 -> String.nsplit phylocsf_answer "\t"
+		| Unix.WEXITED c -> exit c
 		| _ -> raise Exit
 	
 let main () =