build: add back Transcripts (all commented)

_oasis

@@ -75,6 +75,7 @@ Library biocaml
            , Biocaml_wig
            , Biocaml_mzData
            , Biocaml_table
+           , Biocaml_transcripts
   CSources: biocaml_pwm_stub.c, biocaml_mzData_stubs.c
   CCOpt: -O3
 

src/lib/biocaml_transcripts.ml

@@ -1,8 +1,8 @@
 open Biocaml_internal_pervasives
-
-type 'a transcript = { 
-  exons : (int * int) list; 
-  lo : int; 
+(*
+type 'a transcript = {
+  exons : (int * int) list;
+  lo : int;
   hi : int;
   chr : string;
   info : 'a
@@ -18,39 +18,39 @@ end
 module SIIMap = MMap.Make(String)(II)
 module SSMap = MMap.Make(String)(String)
 
-let add_length_to_transcripts transcripts = 
-  let f trx = 
-    let length = 
+let add_length_to_transcripts transcripts =
+  let f trx =
+    let length =
       let g acc (lo,hi) = hi - lo + acc in
-      List.fold_left g 0 trx.exons 
+      List.fold_left g 0 trx.exons
     in
     { trx with info = trx.info,length }
   in
   List.map f transcripts
 
-let of_composite_channel 
-    ?(chr_map=identity) 
-    ?(increment_lo_hi=(0,0)) 
-    ic = 
-  let f acc l = 
+let of_composite_channel
+    ?(chr_map=identity)
+    ?(increment_lo_hi=(0,0))
+    ic =
+  let f acc l =
     let lst = String.nsplit l "\t" in
     let inclo,inchi = increment_lo_hi in
-    let (nm,chr,st,fn) = 
+    let (nm,chr,st,fn) =
       List.nth lst 0,
       chr_map (List.nth lst 1),
       int_of_string (List.nth lst 2) + inclo,
       int_of_string (List.nth lst 3) + inchi
     in
-    let g (nm,chr,st,fn) prev = match prev with 
-      | None -> 
+    let g (nm,chr,st,fn) prev = match prev with
+      | None ->
           {
-            exons = [st,fn]; 
+            exons = [st,fn];
             lo = st;
             hi= fn;
             chr = chr;
             info = nm;
           }
-      | Some trx -> 
+      | Some trx ->
           {
             exons = (st,fn)::(trx.exons);
             lo = if st < trx.lo then st else trx.lo;
@@ -66,29 +66,29 @@ let of_composite_channel
   let ans = List.rev (SSMap.fold folder [] ans) in
   add_length_to_transcripts ans
 
-let of_composite_file ?(chr_map=identity) ?(increment_lo_hi=(0,0)) file = 
+let of_composite_file ?(chr_map=identity) ?(increment_lo_hi=(0,0)) file =
   try_finally
     (of_composite_channel ~chr_map ~increment_lo_hi) close_in (open_in file)
 
-let of_bed_channel ?(chr_map=identity) ?(increment_lo_hi=(1,0)) ic = 
+let of_bed_channel ?(chr_map=identity) ?(increment_lo_hi=(1,0)) ic =
   let bed = Bed.to_list (Bed.of_channel ~chr_map ~increment_lo_hi ic) in
-  let f acc (chr,s,f) = 
+  let f acc (chr,s,f) =
     {
       exons = [s,f];
       lo = s;
       hi = f;
       chr = chr_map chr;
       info = "";
-    }::acc 
+    }::acc
   in
   let ans = List.rev (List.fold_left f [] bed) in
   add_length_to_transcripts ans
 
-let of_bed_file ?(chr_map=identity) ?(increment_lo_hi=(1,0)) file = 
+let of_bed_file ?(chr_map=identity) ?(increment_lo_hi=(1,0)) file =
   try_finally (of_bed_channel ~chr_map ~increment_lo_hi) close_in (open_in file)
 
 let of_gff transcript_name_of_exon gff =
-  let f transcript_name row prev = 
+  let f transcript_name row prev =
     let lo,hi = row.Gff.pos in
     match prev with
       | None -> {
@@ -116,29 +116,29 @@ let of_gff transcript_name_of_exon gff =
   let ans = Gff.fold g StringMap.empty gff in
   StringMap.fold (fun _ x ans -> x::ans) ans []
 
-let all_probes_in 
-    (trx_lst:'a t) 
-    (prbs: (string * int * int * 'b) list) 
+let all_probes_in
+    (trx_lst:'a t)
+    (prbs: (string * int * int * 'b) list)
     : ('a * 'b array) t =
   let insert x prev = match prev with None -> [x] | Some l -> x::l in
-  let siimap_of_exons = 
+  let siimap_of_exons =
     let f acc trx =
       SIIMap.add trx.chr (trx.lo,trx.hi) (trx.exons,trx.info) acc in
     List.fold_left f SIIMap.empty trx_lst
-  in 
-  let stringmap_of_intervaltrees = 
+  in
+  let stringmap_of_intervaltrees =
     let f acc trx = StringMap.add_with trx.chr (insert (trx.lo,trx.hi)) acc in
     let ans = List.fold_left f StringMap.empty trx_lst in
     StringMap.map IntervalTree.create ans
   in
-  let f acc (chr,s,f,v) = 
+  let f acc (chr,s,f,v) =
     let itree = StringMap.find chr stringmap_of_intervaltrees in
     let trxs = IntervalTree.within itree (s,f) in
-    let g accu trx = 
+    let g accu trx =
       let (exons,info) = SIIMap.find chr trx siimap_of_exons in
-      let g_insert (info,u) prev = 
-        match prev with 
-          | None -> info,[v] 
+      let g_insert (info,u) prev =
+        match prev with
+          | None -> info,[v]
           | Some (i,lst) -> (assert (i = info); i,(v::lst))
       in
       match IntervalTree.within (IntervalTree.create exons) (s,f) with
@@ -149,8 +149,8 @@ let all_probes_in
   in
   let ans = List.fold_left f SIIMap.empty prbs in
   let ans = SIIMap.map (fun (info,lst) -> (info,Array.of_list lst)) ans in
-  let f acc trx = 
-    try 
+  let f acc trx =
+    try
       {
         exons = trx.exons;
         lo = trx.lo;
@@ -163,9 +163,9 @@ let all_probes_in
   List.rev (List.fold_left f [] trx_lst)
 
 let all_points_in
-    (trx_lst:'a t) 
+    (trx_lst:'a t)
     (points: (string * int * 'b) list)
     : ('a * 'b array) t =
   let probes = List.map (fun (x,y,z) -> (x,y,y,z)) points in
   all_probes_in trx_lst probes
-
+*)

src/lib/biocaml_transcripts.mli

@@ -1,9 +1,9 @@
 (** Transcripts are integer intervals containing a list of
     exons. Exons are themselves defined as a list of integer intervals. *)
-
-type 'a transcript = { 
-  exons : (int * int) list; 
-  lo : int; 
+(*
+type 'a transcript = {
+  exons : (int * int) list;
+  lo : int;
   hi : int;
   chr : string;
   info : 'a
@@ -27,7 +27,7 @@ val of_bed_file :
     with just a single exon in it, which are the coordinates of the
     transcript itself. Info of type string * int in answer are as in
     [of_composite_file] but the name is always the empty string. *)
-  
+
 val of_gff : (Gff.row -> string option) -> Gff.t -> string t
 (** [of_gff f gff] converts [gff] to a list of [transcript]s. Function
     [f] will be applied to each row in [gff]. If the row is an exon it
@@ -37,7 +37,7 @@ val of_gff : (Gff.row -> string option) -> Gff.t -> string t
     [info] in the answer is the name of the transcript. Raise [Failure] if
     [f] does anything erroneous such as map exons on different chromosomes
     to the same transcript. *)
-  
+
 val all_probes_in : 'a t -> (string * int * int * 'b) list -> ('a * 'b array) t
 (** [all_probes_in transcripts probes] bins [probes] into
     [transcripts]. Each probe in [probes] has a genomic location and value
@@ -48,3 +48,4 @@ val all_probes_in : 'a t -> (string * int * int * 'b) list -> ('a * 'b array) t
 val all_points_in : 'a t -> (string * int * 'b) list -> ('a * 'b array) t
 (** Like [all_probes_in] but the given "probes" are defined on single
     base pairs. *)
+*)