Computing GC content

06_gc/gc.nim

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+import os
+import std/sequtils
+import std/streams
+import nre
+import std/strformat
+
+type
+    DnaString = ref DnaStringObj
+    DnaStringObj = object
+        name: string
+        str: string
+
+let firstLinePattern = re">(\w+)(?:\s+.+)?"
+proc parseNextDnaString(stream: Stream): DnaString =
+    if atEnd(stream):
+        raise newException(ValueError, "Stream is at end")
+
+    let firstLine = readLine(stream)
+    let match = firstLine.match(firstLinePattern)
+    if match.isNone:
+        raise newException(ValueError, "Invalid line: " & firstLine)
+
+    let name = match.get.captures[0]
+    var str = ""
+
+    while not atEnd(stream) and peekChar(stream) != '>':
+        str &= readLine(stream)
+
+    DnaString(name: name, str: str)
+
+proc calcGcContent(dnaString: DnaString): float =
+    let gcCount = dnaString.str.countIt(it == 'G' or it == 'C')
+    return (gcCount / dnaString.str.len) * 100
+
+proc calcMaxGcContent(stream: Stream): (DnaString, float) =
+    var maxGcString: DnaString = nil
+    var maxGcContent = -1.0
+
+    while not atEnd(stream):
+        let str = parseNextDnaString(stream)
+        let gcContent = calcGcContent(str)
+        if gcContent > maxGcContent:
+            maxGcContent = gcContent
+            maxGcString = str
+    
+    return (maxGcString, maxGcContent)
+
+let fileName = paramStr(1)
+let fileStream = newFileStream(fileName)
+if not isNil(fileStream):
+    let maxGcContent = calcMaxGcContent(fileStream)
+    echo $maxGcContent[0].name
+    echo $maxGcContent[1]
+ 
+    fileStream.close()

06_gc/sample.txt

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+>Rosalind_6404
+CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
+TCCCACTAATAATTCTGAGG
+>Rosalind_5959
+CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
+ATATCCATTTGTCAGCAGACACGC
+>Rosalind_0808
+CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
+TGGGAACCTGCGGGCAGTAGGTGGAAT