Initial data commit

Task/Bioinformatics-base-count/Pascal/bioinformatics-base-count.pas

@@ -0,0 +1,77 @@
+program DNA_Base_Count;
+{$IFDEF FPC}
+  {$MODE DELPHI}//String = AnsiString
+{$ELSE}
+  {$APPTYPE CONSOLE}
+{$ENDIF}
+const
+    dna =
+        'CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG' +
+        'CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG' +
+        'AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT' +
+        'GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT' +
+        'CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG' +
+        'TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA' +
+        'TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT' +
+        'CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG' +
+        'TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC' +
+        'GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT';
+var
+  CntIdx : array of NativeUint;
+  DNABases : String;
+  SumBaseTotal : NativeInt;
+
+procedure OutFormatBase(var DNA: String;colWidth:NativeInt);
+var
+  j: NativeInt;
+Begin
+  j := 0;
+  Writeln(' DNA base sequence');
+  While j<Length(DNA) do
+  Begin
+    writeln(j:5,copy(DNA,j+1,colWidth):colWidth+2);
+    inc(j,colWidth);
+  end;
+  writeln;
+end;
+
+procedure Cnt(const DNA: String);
+var
+  i,p :NativeInt;
+Begin
+  SetLength(CntIdx,Length(DNABases));
+  i := 1;
+  while i <= Length(DNA) do
+  Begin
+    p := Pos(DNA[i],DNABases);
+    //found new base so extend list
+    if p = 0 then
+    Begin
+      DNABases := DNABases+DNA[i];
+      p := length(DNABases);
+      Setlength(CntIdx,p+1);
+    end;
+    inc(CntIdx[p]);
+    inc(i);
+  end;
+
+  Writeln('Base     Count');
+  SumBaseTotal := 0;
+  For i := 1 to Length(DNABases) do
+  Begin
+    p := CntIdx[i];
+    inc(SumBaseTotal,p);
+    writeln(DNABases[i]:4,p:10);
+  end;
+  Writeln('Total base count ',SumBaseTotal);
+  writeln;
+end;
+
+var
+  TestDNA: String;
+Begin
+  DNABases :='ACGT';// predefined
+  TestDNA := DNA;
+  OutFormatBase(TestDNA,50);
+  Cnt(TestDNA);
+end.