tweaks to build against batteries 2.x

src/ECM.ml

@@ -6,7 +6,7 @@ Kosiol C, Holmes I and Goldman N. An Empirical Codon Model for Protein Sequence
 However, note that Kosiol et al. presented a 61x61 model while PhyloCSF uses a 64x64 model (including stop codons)
 *)
 
-open Batteries_uni
+open Batteries
 open Printf
 open CamlPaml
 open Expr

src/OmegaModel.ml

@@ -1,6 +1,6 @@
 (** omega (dN/dS) test, similar to using PAML to test for omega<1, but with a few of our own touches *)
 
-open Batteries_uni
+open Batteries
 open Printf
 
 open CamlPaml

src/PhyloCSF.ml

@@ -1,14 +1,14 @@
 (* Wish list: PHYLIP alignment format *)
 
-open Batteries_uni
-open OptParse
+open Batteries
+open Extlib.OptParse
 open Printf
 open CamlPaml
 
 Gsl.Error.init ()
 
-module SMap = Map.StringMap
-module SSet = Set.StringSet
+module SMap = Map.Make(struct type t = string let compare = compare end)
+module SSet = Set.Make(struct type t = string let compare = compare end)
 module Codon = CamlPaml.Code.Codon64
 type strategy = PhyloCSF of [`MaxLik | `FixedLik] | OmegaTest | Nop
 type reading_frame = One | Three | Six
@@ -371,9 +371,9 @@ let parse_kv lines =
 		else
 			try
 				let (k,v) = String.split line "\t"
-				PMap.add k v kv
-			with Not_found -> PMap.add line "" kv
-	fold f PMap.empty lines
+				Map.add k v kv
+			with Not_found -> Map.add line "" kv
+	fold f Map.empty lines
 
 let initialize_strategy () =
 	let paramfile ?(required=true) suffix =
@@ -428,7 +428,7 @@ let initialize_strategy () =
 					if Sys.file_exists fn_config then
 						try
 							let kv = parse_kv (File.lines_of fn_config)
-							Some (float_of_string (PMap.find "omega_H1" kv)), Some (float_of_string (PMap.find "sigma_H1" kv))
+							Some (float_of_string (Map.find "omega_H1" kv)), Some (float_of_string (Map.find "sigma_H1" kv))
 						with
 							| exn -> failwith (sprintf "configuration file %s exists but does not specify valid omega_H1 and sigma_H1 values" fn_config)
 					else

src/PhyloCSFModel.ml

@@ -1,4 +1,4 @@
-open Batteries_uni
+open Batteries
 open Printf
 open CamlPaml
 open CamlPaml.Expr

src/PhyloCSFTest.ml

@@ -2,8 +2,8 @@
 _build/PhyloCSFTest.native "_build/PhyloCSF.native --frames=6 --orf=ATGStop --strategy=fixed" ../PhyloCSF_Parameters/12flies
 *)
 
-open Batteries_uni
-open OptParse
+open Batteries
+open Extlib.OptParse
 open Printf
 open CamlPaml
 
@@ -124,7 +124,7 @@ let mfa headers seqs =
 			Buffer.add_char buf '\n'
 		headers
 		seqs
-	buf
+	Buffer.contents buf
 	
 let open_phylocsf () =
 	let cmd = sprintf "%s %s" fn_exe fp_params
@@ -142,7 +142,7 @@ let main () =
 		flush stdout
 		flush stderr
 		let out = open_phylocsf ()
-		Buffer.output_buffer out aln
+		output_string out aln
 		flush out
 		ignore (Unix.close_process_out out)
 		printf "\n"