Samuel's Tech Blog

import re
import string
 
def main():
    file = open("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa","r")
    gcCount = 0
    totalBaseCount = 0
    for line in file:
        line = line.strip("\n")
        if not line.startswith(">"):
            gcCount += len(re.findall("[GC]", line))
            totalBaseCount += len(re.findall("[GCTA]", line))
    gcFraction = float(gcCount) / totalBaseCount
    print( gcFraction * 100 )
 
 
if __name__ == '__main__':
    main()

import std.stdio;
import std.string;
import std.algorithm;
import std.regex;
 
void main() {
    File file = File("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa","r");
    int gcCount = 0;
    int totalBaseCount = 0;
    string line;
    char c;
    while (!file.eof()) {
        line = file.readln();
        if (line.length > 0 && !startsWith(line, ">")) {
            for(uint i = 0; i < line.length; i++) {
                c = line[i];
                if (c == 'C' || c == 'T' || c == 'G' || c == 'A') {
                    totalBaseCount++;
                    if ( c == 'G' || c == 'C' ) {
                        gcCount++;
                    }
                }   
            }
        }
    }
    float gcFraction = ( cast(float)gcCount / cast(float)totalBaseCount );
    writeln( gcFraction * 100 );
}

#include <string>
#include <fstream>
#include <iostream>
 
int main() {
 
    std::fstream fs("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa", std::ios::in);
 
    int gcCount = 0;
    int totalBaseCount = 0;
 
    if ( fs.is_open() )  {
        std::string line;
        while (std::getline(fs, line)) {
            if(*(line.begin()) != '>') {
                for(std::string::const_iterator pos = line.begin(); pos!=line.end() ; ++pos){
                     switch (*pos){
                       case 'A' :
                         totalBaseCount++;
                         break;
 
                       case 'C' :
                         gcCount++;
                         totalBaseCount++;
                         break;
 
                       case 'G' :
                         gcCount++;
                         totalBaseCount++;
                         break;
 
                       case  'T' :
                         totalBaseCount++;
                         break;
 
                       default:
                         break;
                     }
                }
          }
    }
    //std::cout << "gcCount: " << gcCount << " / totalBaseCount: "<< totalBaseCount << " = " ;
    std::cout << ( (float)gcCount / (float)totalBaseCount ) * 100 << std::endl ;
  } else {
    std::cout << "can't open file" ;
  }
  return 0 ;
}

program gc;
{$mode objfpc} // Do not forget this ever
 
uses
    Sysutils;
 
var
    FastaFile: TextFile;
    CurrentLine: String;
    GCCount: Integer;
    TotalBaseCount: Integer;
    i: Integer;
    c: Char;
    GCFraction: Single;
 
begin
    GCCount := 0;
    TotalBaseCount := 0;
 
    AssignFile(FastaFile, 'Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa'); 
    {$I+} //use exceptions
    try  
        Reset(FastaFile);
        repeat
            Readln(FastaFile, CurrentLine); 
            i := 0;
            while i < Length(CurrentLine) do
            begin
                c := CurrentLine[i];
                if (c = 'A') or (c = 'G') or (c = 'C') or (c = 'T')  then
                begin
                    TotalBaseCount := TotalBaseCount + 1;
                    if (c = 'G') or (c = 'C') then
                        GCCount := GCCount + 1;
                end;
                i := i + 1;
            end;
        until(EOF(FastaFile)); 
        CloseFile(FastaFile);
    except
        on E: EInOutError do
        begin
            Writeln('File handling error occurred. Details: '+E.ClassName+'/'+E.Message);
        end;    
    end;
    GCFraction := GCCount / TotalBaseCount;
    Writeln(FormatFloat('00.0000', GCFraction * 100));
end.

d:
        dmd -ofgc_d_dmd -O -release -inline gc.d
        gdmd -ofgc_d_gdc -O -release -inline gc.d
        ldmd2 -ofgc_d_ldc -O -release -inline gc.d
cpp:
        g++ -ogc_cpp -O3 gc.cpp
 
fpc:
        fpc -ogc_fpc -Ur -O3 -TLINUX gc.pas