Additional problems solved.

Author: kungfucraig

playtime/rosalind/CONS.scala

@@ -0,0 +1,76 @@
+
+
+object CONS extends App {
+  val input = """>Rosalind_1
+ATCCAGCT
+>Rosalind_2
+GGGCAACT
+>Rosalind_3
+ATGGATCT
+>Rosalind_4
+AAGCAACC
+>Rosalind_5
+TTGGAACT
+>Rosalind_6
+ATGCCATT
+>Rosalind_7
+ATGGCACT 
+"""
+  // Outputs:
+  // ATGCAACT
+  // A: 5 1 0 0 5 5 0 0
+  // C: 0 0 1 4 2 0 6 1
+  // G: 1 1 6 3 0 1 0 0
+  // T: 1 5 0 0 0 1 1 6
+  
+  outputConsensusAndProfile(input)
+  
+  def outputConsensusAndProfile(input: String) {
+    val summary : IndexedSeq[Vector[Int]] = summarize(input)
+    val consensus = getConsensus(summary)
+    println(consensus.mkString(""))
+    val profile = getProfile(summary)
+    Vector("A", "C", "G", "T").zip(profile).foreach((x) => 
+      println(String.format("%s: %s", x._1, x._2.mkString(" "))))
+  }
+  
+  def getConsensus(input: IndexedSeq[Vector[Int]]) = {
+    input.map((x) =>
+      x.zipWithIndex.maxBy(_._1)._2 match {
+        case 0 => "A"
+        case 1 => "C"
+        case 2 => "G"
+        case 3 => "T"
+      }
+    )
+  }
+  
+  def getProfile(input: IndexedSeq[Vector[Int]]) = {
+    Range(0, 4).map((i) => input.map((x) => x(i)))
+  }
+  
+  def summarize(input: String) = {
+    val strings = extractDnaStrings(input)
+    val tuples = strings.map(getNucleotideCountTuple)
+    tuples.reduce((x, y) => x.zip(y).map((z) => z._1.zip(z._2).map((w) => w._1 + w._2)))
+  }
+  
+  def getNucleotideCountTuple(dna: String) = {
+    dna.map((x) =>
+      x match {
+        case 'A' => Vector(1, 0, 0, 0)
+        case 'C' => Vector(0, 1, 0, 0)
+        case 'G' => Vector(0, 0, 1, 0)
+        case 'T' => Vector(0, 0, 0, 1)
+      }
+    )
+  }
+  
+  def extractDnaStrings(input: String) = {
+    val re = """>(Rosalind_\d+)\s*([TACG\s]+)\n""".r
+    for(m <- re.findAllIn(input)) 
+        yield m match {
+          case re(name, seq) => seq.replaceAll("""\s+""", "")
+        } 
+  }
+}

playtime/rosalind/MRNA.scala

@@ -0,0 +1,42 @@
+
+object MRNA extends App {
+  val example1 = "MA"
+  val example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
+  val example3 = "MISLGGQRSSSKWNPSNPYYEHFVSDINNALVPEIDWDGGMQAIVFGDIGAILLGELKYMKPFSCCKHKQTKRHTESIWVVDGEEHHYKMFLPEPFNVKEQEEPQWHHKTAAHIYNCLPMAEGMPMLDQWYMFIAAIANTHCWAPRRGTPIHQGELNKEYQDLGMINEHMYICKLCTAIYEGWWTFCTREDNLEELHMTYPKHSFRHRFYFCSAEPTINGIDPVPDRYQWAKFIPYRFVDDSHNNCKHIRNKTSNCCHEWFRAVTWPFMDNTYHRMAHLWGLIYFSNHCANMMIPARMGSPKCTFVKHTQQGGNDSDVPLPVVRNLVWNFYIEDVTKKDRLDGIWPCHMPDDDNCTNFGAMHLHCEGFAEALKVCDSDGTYSAITLFHAWSAKKDDIKGPSDPSTRPRWYMLGQGTFRAMKVTDPSIGQRINNWDPGHVQGHMKAEMHNFWIGSGWDTERMRQHRKEGDMFDDAGVALNGWIWNGYPAGAFRLNMMWQCDGTDAKTQTVHCTWDDPRLCMIKAANSMLRKMWRSFKSPPCHMKDMLQDTLGFICNCYINAVVKHKIAPGKIAWETPQFQLWVTKQMLIFICPVFFIIWIRTNSYCLCIEWYIIPAGVTQFDLSIHVKLKYQQEIFVYLPAGQRKCWLANDQFELNYLSSLRQDQIDSWRWTVHMHGGDHMSPTRDDEARNVLSSDGEWAFYFDDAGSVQMCVEENNQDWVCNKQGGFMRRLTNDVVRKCFKNAHIPCTFEEAHWMEYYVKGMRMLQSCKCGWWVVAGFDYSTCENPGKCSPIINNSSLKFLNPIVDPMWFMWCFMHEKGWWMITLRKTYNNRPFMKKEYVAADECCWLSTTQPVPCDLQDCPFYSDRIYWIHGTSGMCWISPYCQDSPTDCFAYCHIGTREQSIQFGSSQHCFFYNFKHDLKYFSFKASGYFAVVESWLACMDQDWHWYVPCLQPMGEDCLWVTYHCNTHEAEMFWSEITMPLEWLGMAGWIIEASYWIH"
+  
+  val proteinString = example3
+  println(countPossibleRNASequences(proteinString)) 
+
+  def countPossibleRNASequences(protein: String) = {
+    val actual = protein + " "
+    actual.map(proteinToMRna).foldLeft(1L)((z, x) => (z * x.length) % 1000000) 
+    
+  }
+  
+  def proteinToMRna(protein: Char) : List[String] = {
+    protein match {
+      case 'A' => List("GCU", "GCA", "GCC", "GCG")
+      case 'C' => List("UGU", "UGC")
+      case 'D' => List("GAU", "GAC")
+      case 'E' => List("GAA", "GAG")
+      case 'F' => List("UUU", "UUC")
+      case 'G' => List("GGU", "GGC", "GGA", "GGG")
+      case 'H' => List("CAU", "CAC")
+      case 'I' => List("AUU", "AUC", "AUA")
+      case 'K' => List("AAA", "AAG")
+      case 'L' => List("CUU", "CUC", "UUA", "UUG", "CUG", "CUA")
+      case 'M' => List("AUG")
+      case 'N' => List("AAC", "AAU")
+      case 'P' => List("CCU", "CCC", "CCA", "CCG")
+      case 'Q' => List("CAA", "CAG")
+      case 'R' => List("CGU", "CGA", "CGC", "AGA", "CGG", "AGG")
+      case 'S' => List("AGU", "AGC", "UCU", "UCC", "UCG", "UCA")
+      case 'T' => List("ACU", "ACC", "ACA", "ACG")
+      case 'V' => List("GUU", "GUC", "GUA", "GUG")
+      case 'W' => List("UGG")
+      case 'Y' => List("UAU", "UAC")
+      case ' ' => List("UAA", "UAG", "UGA")
+      case _ => throw new RuntimeException("Bad protein")
+    }
+  }
+}