Bioinformatics/base count
Given this string representing ordered DNA bases:
You are encouraged to solve this task according to the task description, using any language you may know.
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
- "Pretty print" the sequence followed by a summary of the counts of each of the bases, (A, C, G, and T) in the sequence as well as the total count of bases in the string.
C
Reads genome from a file, determines string length to ensure optimal formatting <lang C>
- include<string.h>
- include<stdlib.h>
- include<stdio.h>
typedef struct genome{
char* strand; int length; struct genome* next;
}genome;
genome* genomeData; int totalLength = 0, Adenine = 0, Cytosine = 0, Guanine = 0, Thymine = 0;
int numDigits(int num){
int len = 1;
while(num>10){
num = num/10;
len++;
}
return len;
}
void buildGenome(char str[100]){
int len = strlen(str),i; genome *genomeIterator, *newGenome;
totalLength += len;
for(i=0;i<len;i++){
switch(str[i]){
case 'A': Adenine++;
break;
case 'T': Thymine++;
break;
case 'C': Cytosine++;
break;
case 'G': Guanine++;
break;
};
}
if(genomeData==NULL){
genomeData = (genome*)malloc(sizeof(genome));
genomeData->strand = (char*)malloc(len*sizeof(char));
strcpy(genomeData->strand,str);
genomeData->length = len;
genomeData->next = NULL; }
else{
genomeIterator = genomeData;
while(genomeIterator->next!=NULL)
genomeIterator = genomeIterator->next;
newGenome = (genome*)malloc(sizeof(genome));
newGenome->strand = (char*)malloc(len*sizeof(char));
strcpy(newGenome->strand,str);
newGenome->length = len;
newGenome->next = NULL;
genomeIterator->next = newGenome;
}
}
void printGenome(){
genome* genomeIterator = genomeData;
int width = numDigits(totalLength), len = 0;
printf("Sequence:\n");
while(genomeIterator!=NULL){
printf("\n%*d%3s%3s",width+1,len,":",genomeIterator->strand);
len += genomeIterator->length;
genomeIterator = genomeIterator->next; }
printf("\n\nBase Count\n----------\n\n");
printf("%3c%3s%*d\n",'A',":",width+1,Adenine);
printf("%3c%3s%*d\n",'T',":",width+1,Thymine);
printf("%3c%3s%*d\n",'C',":",width+1,Cytosine);
printf("%3c%3s%*d\n",'G',":",width+1,Guanine);
printf("\n%3s%*d\n","Total:",width+1,Adenine + Thymine + Cytosine + Guanine);
free(genomeData);
}
int main(int argc,char** argv) {
char str[100];
int counter = 0, len;
if(argc!=2){
printf("Usage : %s <Gene file name>\n",argv[0]);
return 0;
}
FILE *fp = fopen(argv[1],"r");
while(fscanf(fp,"%s",str)!=EOF)
buildGenome(str);
fclose(fp);
printGenome();
return 0;
} </lang> Run and output :
abhishek_ghosh@Azure:~/doodles$ ./a.out genome.txt Sequence: 0 :CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG 50 :CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG 100 :AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT 150 :GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT 200 :CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG 250 :TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA 300 :TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT 350 :CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG 400 :TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC 450 :GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT Base Count ---------- A : 129 T : 155 C : 97 G : 119 Total: 500
Factor
<lang factor>USING: assocs formatting grouping io kernel literals math math.statistics prettyprint qw sequences sorting ;
CONSTANT: dna $[
qw{
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
} concat
]
- .dna ( seq n -- )
"SEQUENCE:" print [ group ] keep [ * swap " %3d: %s\n" printf ] curry each-index ;
- show-counts ( seq -- )
"BASE COUNTS:" print histogram >alist [ first ] sort-with [ [ " %c: %3d\n" printf ] assoc-each ] [ "TOTAL: " write [ second ] [ + ] map-reduce . ] bi ;
dna [ 50 .dna nl ] [ show-counts ] bi</lang>
- Output:
SEQUENCE:
0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
BASE COUNTS:
A: 129
C: 97
G: 119
T: 155
TOTAL: 500
Go
<lang go>package main
import (
"fmt" "sort"
)
func main() {
dna := "" +
"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" +
"CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" +
"AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" +
"GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" +
"CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" +
"TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" +
"TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" +
"CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" +
"TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" +
"GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"
fmt.Println("SEQUENCE:")
le := len(dna)
for i := 0; i < le; i += 50 {
k := i + 50
if k > le {
k = le
}
fmt.Printf("%5d: %s\n", i, dna[i:k])
}
baseMap := make(map[byte]int) // allows for 'any' base
for i := 0; i < le; i++ {
baseMap[dna[i]]++
}
var bases []byte
for k := range baseMap {
bases = append(bases, k)
}
sort.Slice(bases, func(i, j int) bool { // get bases into alphabetic order
return bases[i] < bases[j]
})
fmt.Println("\nBASE COUNT:")
for _, base := range bases {
fmt.Printf(" %c: %3d\n", base, baseMap[base])
}
fmt.Println(" ------")
fmt.Println(" Σ:", le)
fmt.Println(" ======")
}</lang>
- Output:
SEQUENCE:
0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
BASE COUNT:
A: 129
C: 97
G: 119
T: 155
------
Σ: 500
======
Haskell
<lang haskell>import Data.List (group, sort) import Data.List.Split (chunksOf) import Text.Printf (printf, IsChar(..), PrintfArg(..), fmtChar, fmtPrecision, formatString)
data DNABase = A | C | G | T deriving (Show, Read, Eq, Ord) type DNASequence = [DNABase]
instance IsChar DNABase where
toChar = head . show fromChar = read . pure
instance PrintfArg DNABase where
formatArg x fmt = formatString (show x) (fmt { fmtChar = 's', fmtPrecision = Nothing })
test :: DNASequence test = read . pure <$> concat
[ "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" , "CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" , "AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" , "GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" , "CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" , "TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" , "TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" , "CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" , "TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" , "GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT" ]
chunkedDNASequence :: DNASequence -> [(Int, [DNABase])] chunkedDNASequence = zip [50,100..] . chunksOf 50
baseCounts :: DNASequence -> [(DNABase, Int)] baseCounts = fmap ((,) . head <*> length) . group . sort
main :: IO () main = do
putStrLn "Sequence:" mapM_ (uncurry (printf "%3d: %s\n")) $ chunkedDNASequence test putStrLn "\nBase Counts:" mapM_ (uncurry (printf "%2s: %2d\n")) $ baseCounts test putStrLn (replicate 8 '-') >> printf " Σ: %d\n\n" (length test)</lang>
- Output:
Sequence: 50: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG 100: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG 150: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT 200: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT 250: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG 300: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA 350: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT 400: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG 450: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC 500: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT Base Counts: A: 129 C: 97 G: 119 T: 155 -------- Σ: 500
Java
<lang Java> import java.util.*;
public class orderedSequence {
public static void main(String[] args) {
Sequence gene = new Sequence("CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATATTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTATCGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTGTCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGACGACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT");
gene.runSequence();
} }
//separate class for defining behaviors public class Sequence {
private String seq;
public Sequence(String sq) {
this.seq = sq; }
//turn sequence string into an array of characters public char[] getSequence() { char[] list = seq.toCharArray(); return list; }
//print the organized structure of the sequence public void prettyPrint() {
char[] l = this.getSequence(); int i = 0; System.out.println("Sequence: \n");
while(i < l.length - 1) { System.out.println("" + i + " : " + Arrays.toString(Arrays.copyOfRange(l, i, i + 50)) + "\n"); i += 50; } }
//count the frequency of each of the bases public Map countBases() {
Map<String, Integer> counter = new HashMap<>(); counter.put("Sum", 0); counter.put("A", 0); char[] bases = this.getSequence(); for(char c : bases) { counter.put("Sum", counter.get("Sum") + 1); if(!counter.containsKey(String.valueOf(c))) counter.put(String.valueOf(c), 1); else counter.put(String.valueOf(c), counter.get(String.valueOf(c)) + 1); } return counter; }
//display a base vs. frequency chart public void displayCount() { Map<String, Integer> c = this.countBases(); System.out.println("Base vs. Count: \n"); c.forEach((String,Integer)->System.out.println(String + " : " + Integer + "\n")); }
public void runSequence() { this.prettyPrint(); this.displayCount(); } }
</lang>
- Output:
Sequence: 0 : [C, G, T, A, A, A, A, A, A, T, T, A, C, A, A, C, G, T, C, C, T, T, T, G, G, C, T, A, T, C, T, C, T, T, A, A, A, C, T, C, C, T, G, C, T, A, A, A, T, G] 50 : [C, T, C, G, T, G, C, T, T, T, C, C, A, A, T, T, A, T, G, T, A, A, G, C, G, T, T, C, C, G, A, G, A, C, G, G, G, G, T, G, G, T, C, G, A, T, T, C, T, G] 100 : [A, G, G, A, C, A, A, A, G, G, T, C, A, A, G, A, T, G, G, A, G, C, G, C, A, T, C, G, A, A, C, G, C, A, A, T, A, A, G, G, A, T, C, A, T, T, T, G, A, T] 150 : [G, G, G, A, C, G, T, T, T, C, G, T, C, G, A, C, A, A, A, G, T, C, T, T, G, T, T, T, C, G, A, G, A, G, T, A, A, C, G, G, C, T, A, C, C, G, T, C, T, T] 200 : [C, G, A, T, T, C, T, G, C, T, T, A, T, A, A, C, A, C, T, A, T, G, T, T, C, T, T, A, T, G, A, A, A, T, G, G, A, T, G, T, T, C, T, G, A, G, T, T, G, G] 250 : [T, C, A, G, T, C, C, C, A, A, T, G, T, G, C, G, G, G, G, T, T, T, C, T, T, T, T, A, G, T, A, C, G, T, C, G, G, G, A, G, T, G, G, T, A, T, T, A, T, A] 300 : [T, T, T, A, A, T, T, T, T, T, C, T, A, T, A, T, A, G, C, G, A, T, C, T, G, T, A, T, T, T, A, A, G, C, A, A, T, T, C, A, T, T, T, A, G, G, T, T, A, T] 350 : [C, G, C, C, G, C, G, A, T, G, C, T, C, G, G, T, T, C, G, G, A, C, C, G, C, C, A, A, G, C, A, T, C, T, G, G, C, T, C, C, A, C, T, G, C, T, A, G, T, G] 400 : [T, C, C, T, A, A, A, T, T, T, G, A, A, T, G, G, C, A, A, A, C, A, C, A, A, A, T, A, A, G, A, T, T, T, A, G, C, A, A, T, T, C, G, T, G, T, A, G, A, C] 450 : [G, A, C, C, G, G, G, G, A, C, T, T, G, C, A, T, G, A, T, G, G, G, A, G, C, A, G, C, T, T, T, G, T, T, A, A, A, C, T, A, C, G, A, A, C, G, T, A, A, T] Base vs. Count: A : 129 C : 97 T : 155 G : 119 Sum : 500
Julia
<lang julia>const sequence = "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" * "CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" * "AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" * "GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" * "CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" * "TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" * "TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" * "CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" * "TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" * "GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"
function dnasequenceprettyprint(seq, colsize=50)
println(length(seq), "nt DNA sequence:\n")
rows = [seq[i:min(length(seq), i + colsize - 1)] for i in 1:colsize:length(seq)]
for (i, r) in enumerate(rows)
println(lpad(colsize * (i - 1), 5), " ", r)
end
end
dnasequenceprettyprint(sequence)
function printcounts(seq)
bases = [['A', 0], ['C', 0], ['G', 0], ['T', 0]]
for c in seq, base in bases
if c == base[1]
base[2] += 1
end
end
println("\nNucleotide counts:\n")
for base in bases
println(lpad(base[1], 10), lpad(string(base[2]), 12))
end
println(lpad("Other", 10), lpad(string(length(seq) - sum(x[2] for x in bases)), 12))
println(" _________________\n", lpad("Total", 10), lpad(string(length(seq)), 12))
end
printcounts(sequence)
</lang>
- Output:
500nt DNA sequence:
0 CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50 CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100 AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150 GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200 CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250 TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300 TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350 CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400 TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450 GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
Nucleotide counts:
A 129
C 97
G 119
T 155
Other 0
_________________
Total 500
Pascal
<lang pascal>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.</lang>
- Output:
DNA base sequence
0 CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50 CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100 AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150 GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200 CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250 TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300 TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350 CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400 TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450 GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
Base Count
A 129
C 97
G 119
T 155
Total base count 500
Perl
<lang perl>use strict; use warnings; use feature 'say';
my %cnt; my $total = 0;
while ($_ = ) {
chomp;
printf "%4d: %s\n", $total+1, s/(.{10})/$1 /gr;
$total += length;
$cnt{$_}++ for split //
}
say "\nTotal bases: $total"; say "$_: " . ($cnt{$_}//0) for <A C G T>;
__DATA__ CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT</lang>
- Output:
1: CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG 51: CTCGTGCTTT CCAATTATGT AAGCGTTCCG AGACGGGGTG GTCGATTCTG 101: AGGACAAAGG TCAAGATGGA GCGCATCGAA CGCAATAAGG ATCATTTGAT 151: GGGACGTTTC GTCGACAAAG TCTTGTTTCG AGAGTAACGG CTACCGTCTT 201: CGATTCTGCT TATAACACTA TGTTCTTATG AAATGGATGT TCTGAGTTGG 251: TCAGTCCCAA TGTGCGGGGT TTCTTTTAGT ACGTCGGGAG TGGTATTATA 301: TTTAATTTTT CTATATAGCG ATCTGTATTT AAGCAATTCA TTTAGGTTAT 351: CGCCGCGATG CTCGGTTCGG ACCGCCAAGC ATCTGGCTCC ACTGCTAGTG 401: TCCTAAATTT GAATGGCAAA CACAAATAAG ATTTAGCAAT TCGTGTAGAC 451: GACCGGGGAC TTGCATGATG GGAGCAGCTT TGTTAAACTA CGAACGTAAT Total bases: 500 A: 129 C: 97 G: 119 T: 155
Phix
<lang Phix>constant dna = substitute(""" CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT ""","\n","") sequence acgt = repeat(0,5) for i=1 to length(dna) do
acgt[find(dna[i],"ACGT")] += 1
end for acgt[$] = sum(acgt) sequence s = split(trim(join_by(split(join_by(dna,1,10,""),"\n"),1,5," ")),"\n") for i=1 to length(s) do
printf(1,"%3d: %s\n",{(i-1)*50+1,s[i]})
end for printf(1,"\nBase counts: A:%d, C:%d, G:%d, T:%d, total:%d\n",acgt)</lang>
- Output:
1: CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG 51: CTCGTGCTTT CCAATTATGT AAGCGTTCCG AGACGGGGTG GTCGATTCTG 101: AGGACAAAGG TCAAGATGGA GCGCATCGAA CGCAATAAGG ATCATTTGAT 151: GGGACGTTTC GTCGACAAAG TCTTGTTTCG AGAGTAACGG CTACCGTCTT 201: CGATTCTGCT TATAACACTA TGTTCTTATG AAATGGATGT TCTGAGTTGG 251: TCAGTCCCAA TGTGCGGGGT TTCTTTTAGT ACGTCGGGAG TGGTATTATA 301: TTTAATTTTT CTATATAGCG ATCTGTATTT AAGCAATTCA TTTAGGTTAT 351: CGCCGCGATG CTCGGTTCGG ACCGCCAAGC ATCTGGCTCC ACTGCTAGTG 401: TCCTAAATTT GAATGGCAAA CACAAATAAG ATTTAGCAAT TCGTGTAGAC 451: GACCGGGGAC TTGCATGATG GGAGCAGCTT TGTTAAACTA CGAACGTAAT Base counts: A:129, C:97, G:119, T:155, total:500
Python
Procedural
<lang python>from collections import Counter
def basecount(dna):
return sorted(Counter(dna).items())
def seq_split(dna, n=50):
return [dna[i: i+n] for i in range(0, len(dna), n)]
def seq_pp(dna, n=50):
for i, part in enumerate(seq_split(dna, n)):
print(f"{i*n:>5}: {part}")
print("\n BASECOUNT:")
tot = 0
for base, count in basecount(dna):
print(f" {base:>3}: {count}")
tot += count
base, count = 'TOT', tot
print(f" {base:>3}= {count}")
if __name__ == '__main__':
print("SEQUENCE:")
sequence = \
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG\ CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG\ AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT\ GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT\ CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG\ TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA\ TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT\ CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG\ TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC\ GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
seq_pp(sequence)
</lang>
- Output:
SEQUENCE:
0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
BASECOUNT:
A: 129
C: 97
G: 119
T: 155
TOT= 500
Functional
Sequence and base counts displayed in GenBank format.
<lang python>Bioinformatics – base count
from itertools import count from functools import reduce
- genBankFormatWithBaseCounts :: String -> String
def genBankFormatWithBaseCounts(sequence):
DNA Sequence displayed in a subset of the GenBank format.
See example at foot of:
https://www.genomatix.de/online_help/help/sequence_formats.html
ks, totals = zip(*baseCounts(sequence))
ns = list(map(str, totals))
w = 2 + max(map(len, ns))
return '\n'.join([
'DEFINITION len=' + str(sum(totals)),
'BASE COUNT ' + .join(
n.rjust(w) + ' ' + k.lower() for (k, n)
in zip(ks, ns)
),
'ORIGIN'
] + [
str(i).rjust(9) + ' ' + k for i, k
in zip(
count(1, 60),
[
' '.join(row) for row in
chunksOf(6)(chunksOf(10)(sequence))
]
)
] + ['//'])
- baseCounts :: String -> Zip [(String, Int)]
def baseCounts(baseString):
Sums for each base type in the given sequence string, with
a fifth sum for any characters not drawn from {A, C, G, T}.
bases = {
'A': 0,
'C': 1,
'G': 2,
'T': 3
}
return zip(
list(bases.keys()) + ['Other'],
foldl(
lambda a: compose(
nthArrow(succ)(a),
flip(curry(bases.get))(4)
)
)((0, 0, 0, 0, 0))(baseString)
)
- -------------------------- TEST --------------------------
- main :: IO ()
def main():
Base counts and sequence displayed in GenBank format
print(
genBankFormatWithBaseCounts(\
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG\ CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG\ AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT\ GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT\ CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG\ TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA\ TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT\ CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG\ TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC\ GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT)
)
- ------------------------ GENERIC -------------------------
- chunksOf :: Int -> [a] -> a
def chunksOf(n):
A series of lists of length n, subdividing the
contents of xs. Where the length of xs is not evenly
divible, the final list will be shorter than n.
return lambda xs: reduce(
lambda a, i: a + [xs[i:n + i]],
range(0, len(xs), n), []
) if 0 < n else []
- compose :: ((a -> a), ...) -> (a -> a)
def compose(*fs):
Composition, from right to left,
of a series of functions.
def go(f, g):
def fg(x):
return f(g(x))
return fg
return reduce(go, fs, lambda x: x)
- curry :: ((a, b) -> c) -> a -> b -> c
def curry(f):
A curried function derived
from an uncurried function.
return lambda x: lambda y: f(x, y)
- flip :: (a -> b -> c) -> b -> a -> c
def flip(f):
The (curried or uncurried) function f with its
arguments reversed.
return lambda a: lambda b: f(b)(a)
- foldl :: (a -> b -> a) -> a -> [b] -> a
def foldl(f):
Left to right reduction of a list,
using the binary operator f, and
starting with an initial value a.
def go(acc, xs):
return reduce(lambda a, x: f(a)(x), xs, acc)
return lambda acc: lambda xs: go(acc, xs)
- nthArrow :: (a -> b) -> Tuple -> Int -> Tuple
def nthArrow(f):
A simple function lifted to one which applies
to a tuple, transforming only its nth value.
def go(v, n):
return v if n > len(v) else [
x if n != i else f(x)
for i, x in enumerate(v)
]
return lambda tpl: lambda n: tuple(go(tpl, n))
- succ :: Enum a => a -> a
def succ(x):
The successor of a value.
For numeric types, (1 +).
return 1 + x
- MAIN ---
if __name__ == '__main__':
main()</lang>
- Output:
DEFINITION len=500
BASE COUNT 129 a 97 c 119 g 155 t 0 other
ORIGIN
1 CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG CTCGTGCTTT
61 CCAATTATGT AAGCGTTCCG AGACGGGGTG GTCGATTCTG AGGACAAAGG TCAAGATGGA
121 GCGCATCGAA CGCAATAAGG ATCATTTGAT GGGACGTTTC GTCGACAAAG TCTTGTTTCG
181 AGAGTAACGG CTACCGTCTT CGATTCTGCT TATAACACTA TGTTCTTATG AAATGGATGT
241 TCTGAGTTGG TCAGTCCCAA TGTGCGGGGT TTCTTTTAGT ACGTCGGGAG TGGTATTATA
301 TTTAATTTTT CTATATAGCG ATCTGTATTT AAGCAATTCA TTTAGGTTAT CGCCGCGATG
361 CTCGGTTCGG ACCGCCAAGC ATCTGGCTCC ACTGCTAGTG TCCTAAATTT GAATGGCAAA
421 CACAAATAAG ATTTAGCAAT TCGTGTAGAC GACCGGGGAC TTGCATGATG GGAGCAGCTT
481 TGTTAAACTA CGAACGTAAT
//
Racket
<lang racket>#lang racket
(define (fold-sequence seq kons #:finalise (finalise (λ x (apply values x))) . k0s)
(define (recur seq . ks)
(if (null? seq)
(call-with-values (λ () (apply finalise ks)) (λ vs (apply values vs)))
(call-with-values (λ () (apply kons (car seq) ks)) (λ ks+ (apply recur (cdr seq) ks+)))))
(apply recur (if (string? seq) (string->list (regexp-replace* #px"[^ACGT]" seq "")) seq) k0s))
(define (sequence->pretty-printed-string seq)
(define (fmt idx cs-rev) (format "~a: ~a" (~a idx #:width 3 #:align 'right) (list->string (reverse cs-rev))))
(fold-sequence
seq
(λ (b n start-idx lns-rev cs-rev)
(if (zero? (modulo n 50))
(values (+ n 1) n (if (pair? cs-rev) (cons (fmt start-idx cs-rev) lns-rev) lns-rev) (cons b null)) (values (+ n 1) start-idx lns-rev (cons b cs-rev))))
0 0 null null #:finalise (λ (n idx lns-rev cs-rev)
(string-join (reverse (if (null? cs-rev) lns-rev (cons (fmt idx cs-rev) lns-rev))) "\n"))))
(define (count-bases b as cs gs ts n)
(values (+ as (if (eq? b #\A) 1 0))
(+ cs (if (eq? b #\C) 1 0)) (+ gs (if (eq? b #\T) 1 0)) (+ ts (if (eq? b #\G) 1 0)) (add1 n)))
(define (bioinformatics-Base_count s)
(define-values (as cs gs ts n) (fold-sequence s count-bases 0 0 0 0 0)) (printf "SEQUENCE:~%~%~a~%~%" (sequence->pretty-printed-string s)) (printf "BASE COUNT:~%-----------~%~%~a~%~%"
(string-join (map (λ (c n) (format " ~a :~a" c (~a #:width 4 #:align 'right n))) '(A T C G) (list as ts cs gs)) "\n"))
(newline) (printf "TOTAL: ~a~%" n))
(module+
main (define the-string #<<EOS
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT EOS )
(bioinformatics-Base_count the-string))</lang>
- Output:
SEQUENCE: 0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG 50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG 100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT 150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT 200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG 250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA 300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT 350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG 400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC 450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT BASE COUNT: ----------- A : 129 T : 119 C : 97 G : 155 TOTAL: 500
Raku
(formerly Perl 6)
It's the Letter frequency task all over again, just simpler and dressed up in different clothes.
The specs for what "pretty print" means are sadly lacking. Ah well, just makes it easily defensible if I do anything at all.
<lang perl6>my $dna = join , lines q:to/END/;
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT END
put pretty($dna, 80);
put "\nTotal bases: ", +my $bases = $dna.comb.Bag;
put $bases.sort(~*.key).join: "\n";
sub pretty ($string, $wrap = 50) {
$string.comb($wrap).map( { sprintf "%8d: %s", $++ * $wrap, $_ } ).join: "\n"
}</lang>
- Output:
0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCG
80: AGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTC
160: GTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGT
240: TCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATATTTAATTTTTCTATATAGCG
320: ATCTGTATTTAAGCAATTCATTTAGGTTATCGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGACGACCGGGGACTTGCATGATGGGAGCAGCTT
480: TGTTAAACTACGAACGTAAT
Total bases: 500
A 129
C 97
G 119
T 155
REXX
A little extra boilerplate was added to verify correct coding of the bases in a DNA string and the alignment of the (totals) numbers. <lang rexx>/*REXX program finds the number of each base in a DNA string (along with a total). */ parse arg dna . if dna== | dna=="," then dna= 'cgtaaaaaattacaacgtcctttggctatctcttaaactcctgctaaatg' ,
'ctcgtgctttccaattatgtaagcgttccgagacggggtggtcgattctg' ,
'aggacaaaggtcaagatggagcgcatcgaacgcaataaggatcatttgat' ,
'gggacgtttcgtcgacaaagtcttgtttcgagagtaacggctaccgtctt' ,
'cgattctgcttataacactatgttcttatgaaatggatgttctgagttgg' ,
'tcagtcccaatgtgcggggtttcttttagtacgtcgggagtggtattata' ,
'tttaatttttctatatagcgatctgtatttaagcaattcatttaggttat' ,
'cgccgcgatgctcggttcggaccgccaagcatctggctccactgctagtg' ,
'tcctaaatttgaatggcaaacacaaataagatttagcaattcgtgtagac' ,
'gaccggggacttgcatgatgggagcagctttgttaaactacgaacgtaat'
dna= space(dna, 0); upper dna /*elide blanks from DNA; uppercase it. */ say '────────length of the DNA string: ' length(dna) @.= 0 /*initialize the count for all bases. */ w= 1 /*the maximum width of a base count. */ $= /*a placeholder for the names of bases.*/
do j=1 for length(dna) /*traipse through the DNA string. */
_= substr(dna, j, 1) /*obtain a base name from the DNA str. */
if pos(_, $)==0 then $= $ || _ /*if not found before, add it to list. */
@._= @._ + 1 /*bump the count of this base. */
w= max(w, length(@._) ) /*compute the maximum width number. */
end /*j*/
say
do k=0 for 255; z= d2c(k) /*traipse through all possibilities. */
if pos(z, $)==0 then iterate /*Was this base found? No, then skip. */
say ' base ' z " has a basecount of: " right(@.z, w)
@.tot= @.tot + @.z /*add to a grand total to verify count.*/
end /*k*/ /*stick a fork in it, we're all done. */
say say '────────total for all basecounts:' right(@.tot, w+1)</lang>
- output when using the default input:
────────length of the DNA string: 500
base A has a basecount of: 129
base C has a basecount of: 97
base G has a basecount of: 119
base T has a basecount of: 155
────────total for all basecounts: 500
Ring
<lang ring> dna = "" +
"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" +
"CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" +
"AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" +
"GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" +
"CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" +
"TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" +
"TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" +
"CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" +
"TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" +
"GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"
dnaBase = [:A=0, :C=0, :G=0, :T=0] lenDna = len(dna) for n = 1 to lenDna
dnaStr = substr(dna,n,1)
switch dnaStr
on "A"
strA = dnaBase["A"]
strA++
dnaBase["A"] = strA
on "C"
strC = dnaBase["C"]
strC++
dnaBase["C"] = strC
on "G"
strG = dnaBase["G"]
strG++
dnaBase["G"] = strG
on "T"
strT = dnaBase["T"]
strT++
dnaBase["T"] = strT
off
next ? "A : " + dnaBase["A"] ? "T : " + dnaBase["T"] ? "C : " + dnaBase["C"] ? "G : " + dnaBase["G"] </lang>
- Output:
A : 129 T : 155 C : 97 G : 119
Swift
<lang swift>import Foundation
let dna = """
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
"""
print("input:\n\(dna)\n")
let counts =
dna.replacingOccurrences(of: "\n", with: "").reduce(into: [:], { $0[$1, default: 0] += 1 })
print("Counts: \(counts)") print("Total: \(counts.values.reduce(0, +))")</lang>
- Output:
input: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT ["C": 97, "T": 155, "G": 119, "A": 129] Total: 500
Wren
<lang ecmascript>import "/fmt" for Fmt import "/sort" for Sort import "/trait" for Stepped
var dna = "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" +
"CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" +
"AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" +
"GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" +
"CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" +
"TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" +
"TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" +
"CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" +
"TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" +
"GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"
System.print("SEQUENCE:") var le = dna.count for (i in Stepped.new(0...le, 50)) {
var k = i + 50
if (k > le) k = le
System.print("%(Fmt.d(5, i)): %(dna[i...k])")
} var baseMap = {} // allows for 'any' base for (i in 0...le) {
var d = dna[i] var v = baseMap[d] baseMap[d] = !v ? 1 : v + 1
} var bases = baseMap.keys.toList Sort.quick(bases)
System.print("\nBASE COUNT:") for (base in bases) {
System.print(" %(base): %(Fmt.d(3, baseMap[base]))")
} System.print(" ------") System.print(" Σ: %(le)") System.print(" ======")</lang>
- Output:
SEQUENCE:
0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
BASE COUNT:
A: 129
C: 97
G: 119
T: 155
------
Σ: 500
======
zkl
<lang zkl>bases:=
- <<<"
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT" - " \n";
- <<<
[0..*,50].zipWith(fcn(n,bases){ println("%6d: %s".fmt(n,bases.concat())) },
bases.walker().walk.fp(50)).pump(Void); // .pump forces the iterator
println("\nBase Counts: ", bases.counts().pump(String,Void.Read,"%s: %d ".fmt)); println("Total: ",bases.len());</lang>
- Output:
0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
Base Counts: A: 129 C: 97 G: 119 T: 155
Total: 500