Add reverseComplement function to all BioCollections.

Fix: #65 and #66

docsrc/content/MAF.fsx

@@ -0,0 +1,71 @@
+(*** hide ***)
+// This block of code is omitted in the generated HTML documentation. Use 
+// it to define helpers that you do not want to show in the documentation.
+#I @"../../bin/BioFSharp/net47/"
+#I @"../../bin/BioFSharp.BioDB/net45/"
+#I @"../../bin/BioFSharp.ImgP/net47"
+#I @"../../bin/BioFSharp.IO/net47/"
+#I @"../../bin/BioFSharp.Parallel/net47/"
+#I @"../../bin/BioFSharp.Stats/net47/"
+#I @"../../bin/BioFSharp.Vis/net47/"
+#r @"../../lib/Formatting/FSharp.Plotly.dll"
+#r "BioFSharp.dll"
+#r "BioFSharp.IO.dll"
+#r "FSharpAux.dll"
+#r "FSharpAux.IO.dll"
+
+(** 
+
+
+*)
+open System
+open FSharpAux
+open FSharpAux.IO
+open BioFSharp.IO
+
+let fileDir = __SOURCE_DIRECTORY__ + "/data/"
+
+// http://www.bx.psu.edu/~dcking/man/maf.xhtml
+
+
+/// Reads FastaItem from file. Converter determines type of sequence by converting seq<char> -> type
+let fromFileEnumerator (converter:seq<char>-> 'a) (fileEnumerator) =
+
+    // Conditon of grouping lines
+    let same_group l =             
+        not (String.length l = 0 || l.[0] <> 'a')
+
+    // Matches grouped lines and concatenates them
+    let record d (converter:seq<char>-> 'a) = 
+        match d with
+        | [] -> raise (System.Exception "Incorrect MAF format")
+        | (h:string) :: l when h.StartsWith "a" ->  let header = h .Remove(0,1)
+                                                    let line = (Seq.concat l) |> converter
+                                                    h,l
+                                                    //createFastaItem header sequence
+
+        | h :: _ -> raise (System.Exception "Incorrect MAF format")        
+
+    // main
+    fileEnumerator
+    |> Seq.filter (fun (l:string) -> not (l.StartsWith " " || l.StartsWith "#"))
+    //|> Seq.filter (fun (l:string) -> not (l.Length < 1))
+
+    |> Seq.groupWhen same_group 
+    |> Seq.map (fun l -> record (List.ofSeq l) converter)
+
+
+/// Reads FastaItem from file. Converter determines type of sequence by converting seq<char> -> type
+let fromFile converter (filePath) =
+    FileIO.readFile filePath
+    |> fromFileEnumerator converter
+
+
+fromFile id (fileDir + "alignment.maf") |> Seq.length
+
+
+
+
+
+//let rec parseS src start size strand srcSize text =
+

docsrc/content/data/alignment.maf

@@ -0,0 +1,22 @@
+##maf version=1 scoring=tba.v8 
+# tba.v8 (((human chimp) baboon) (mouse rat)) 
+
+a score=23262.0     
+s hg18.chr7    27578828 38 + 158545518 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
+s panTro1.chr6 28741140 38 + 161576975 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
+s baboon         116834 38 +   4622798 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG
+s mm4.chr6     53215344 38 + 151104725 -AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG
+s rn3.chr4     81344243 40 + 187371129 -AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG
+
+a score=5062.0                    
+s hg18.chr7    27699739 6 + 158545518 TAAAGA
+s panTro1.chr6 28862317 6 + 161576975 TAAAGA
+s baboon         241163 6 +   4622798 TAAAGA 
+s mm4.chr6     53303881 6 + 151104725 TAAAGA
+s rn3.chr4     81444246 6 + 187371129 taagga
+
+a score=6636.0
+s hg18.chr7    27707221 13 + 158545518 gcagctgaaaaca
+s panTro1.chr6 28869787 13 + 161576975 gcagctgaaaaca
+s baboon         249182 13 +   4622798 gcagctgaaaaca
+s mm4.chr6     53310102 13 + 151104725 ACAGCTGAAAATA

src/BioFSharp/BioArray.fs

@@ -40,7 +40,17 @@ module BioArray =
         |> Seq.toArray
 
 
+    /// Create the reverse DNA or RNA strand. For example, the sequence "ATGC" is converted to "CGTA"
+    let reverse (nucs:BioArray<Nucleotides.Nucleotide>) = 
+        nucs |> Array.rev
 
+    /// Create the complement DNA or cDNA (from RNA) strand. For example, the sequence "ATGC" is converted to "TACG"
+    let complement (nucs:BioArray<Nucleotides.Nucleotide>) = 
+        nucs |> Array.map Nucleotides.complement
+
+    /// Create the reverse complement strand meaning antiparallel DNA strand or the cDNA (from RNA) respectivly. For example, the sequence "ATGC" is converted to "GCAT". "Antiparallel" combines the two functions "Complement" and "Inverse".
+    let reverseComplement (nucs:BioArray<Nucleotides.Nucleotide>) = 
+        nucs |> Array.map Nucleotides.complement |> Array.rev
 
 
     /// Builts a new collection whose elements are the result of applying

src/BioFSharp/BioList.fs

@@ -43,6 +43,18 @@ module BioList =
         |> Seq.choose OptionConverter.charToOptionNucleotid           
         |> Seq.toList
 
+
+    /// Create the reverse DNA or RNA strand. For example, the sequence "ATGC" is converted to "CGTA"
+    let reverse (nucs:BioList<Nucleotides.Nucleotide>) = 
+        nucs |> List.rev
+
+    /// Create the complement DNA or cDNA (from RNA) strand. For example, the sequence "ATGC" is converted to "TACG"
+    let complement (nucs:BioList<Nucleotides.Nucleotide>) = 
+        nucs |> List.map Nucleotides.complement
+
+    /// Create the reverse complement strand meaning antiparallel DNA strand or the cDNA (from RNA) respectivly. For example, the sequence "ATGC" is converted to "GCAT". "Antiparallel" combines the two functions "Complement" and "Inverse".
+    let reverseComplement (nucs:BioList<Nucleotides.Nucleotide>) = 
+        nucs |> List.map Nucleotides.complement |> List.rev
 
 //    /// Builts a new collection whose elements are the result of applying
 //    /// the given function to each triplet of the collection. 

src/BioFSharp/BioSeq.fs

@@ -62,13 +62,24 @@ module BioSeq =
                 | _         -> sourceIsEmpty := true                               
         }
 
+
+    /// Create the reverse DNA or RNA strand. For example, the sequence "ATGC" is converted to "CGTA"
+    let reverse (nucs:seq<Nucleotides.Nucleotide>) = 
+        nucs |> Seq.rev
+
+    /// Create the complement DNA or cDNA (from RNA) strand. For example, the sequence "ATGC" is converted to "TACG"
+    let complement (nucs:seq<Nucleotides.Nucleotide>) = 
+        nucs |> Seq.map Nucleotides.complement
+
+    /// Create the reverse complement strand meaning antiparallel DNA strand or the cDNA (from RNA) respectivly. For example, the sequence "ATGC" is converted to "GCAT". "Antiparallel" combines the two functions "Complement" and "Inverse".
+    let reverseComplement (nucs:seq<Nucleotides.Nucleotide>) = 
+        nucs |> Seq.map Nucleotides.complement |> Seq.rev
+
     //  Replace T by U
     /// Transcribe a given DNA coding strand (5'-----3')
     let transcribeCodeingStrand (nucs:seq<Nucleotides.Nucleotide>) = 
         nucs |> Seq.map (fun nuc -> Nucleotides.replaceTbyU nuc)
 
-
-
     //  
     /// Transcribe a given DNA template strand (3'-----5')
     let transcribeTemplateStrand (nucs:seq<Nucleotides.Nucleotide>) = 

src/BioFSharp/Nucleotides.fs

@@ -270,7 +270,7 @@ module Nucleotides =
 
 
 
-    /// Create the complement DNA or RNA strand. For example, the sequence "ATGC" is converted to "TACG"
+    /// Returns the Nucleotide from the complementary strand 
     let complement (nuc:Nucleotide) =
         match nuc with
         | A    -> T 
@@ -289,34 +289,6 @@ module Nucleotides =
         | _    -> nuc
 
 
-    /// Create the inverse DNA or RNA strand. For example, the sequence "ATGC" is converted to "CGTA"
-    let inverse (nuc:Nucleotide) =           
-        match nuc with
-        | A -> C
-        | T -> G
-        | G -> T 
-        | C -> A
-
-        | U -> A        
-
-        // 'Ambiguous Nucleotide Codes: double base codes
-        | R -> W
-        | Y -> S
-        | K -> M
-        | M -> K
-        | S -> Y
-        | W -> R
-        // 'Ambiguous Nucleotide Codes: triple base codes
-        | B -> V
-        | D -> H
-        | H -> D
-        | V -> B
-
-        | _    -> nuc
-
-    /// Create the antiparallel DNA or RNA strand. For example, the sequence "ATGC" is converted to "GCAT". "Antiparallel" combines the two functions "Complement" and "Inverse".
-    let antiparallel (nuc:Nucleotide) = 
-        inverse (complement nuc)
 
 
     /// Replace thymidine (T) by uracil (U). For example, the sequence "ATUGC" is converted to "AUUGC".