gatoravi · September 30, 2019 23:33 · gatoravi · Sep 28, 2019 · gatoravi · Sep 29, 2019
diff --git a/2mer.cc b/2mer.cc
 /*
 Copyright 2019 Avinash Ramu

 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

 The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

 //Takes a kmer and fasta as input and lists all positions
 //within the fasta for that kmer.
 //Example usage ./a.out hg38.fa AT
 #include <iostream>
 #include <fstream>
 #include <sstream>

 using namespace std;

 int main(int argc, char* argv[]) {
    if (argc != 3) {
        cerr << "Example usage ./a.out hg38.fa AT";
        return 1;
    }
    string kmer = argv[2];

    // Read the FASTA
    ifstream fasta_fh(argv[1]);
    std::string line, contig;
    long position;
    char prev_line_last_char; // STore the last character of previous line
    int line_number = 0;
    while(std::getline(fasta_fh, line).good()) {
        if (line[0] == '>') {
            istringstream iss(line.substr(1));
            iss >> contig; // Get the chromosome name
            prev_line_last_char = '0';
            position = 0;
            continue;
        }
        for (std::string::size_type i = 0; i < line.size(); i++) {
            position += 1;
            if(i == 0 && prev_line_last_char != '0') { //CHeck concatenation with prev line
                string first;
                first += prev_line_last_char;
                first += line[0];
                if(first == kmer) {
                    cout << contig << " " << position << endl;
                }
            }
            string twomer; //Compare consecutive characters
            twomer += line[i];
            twomer += line[i+1];
            if(twomer == kmer) { // Check if the 2mer is what we want
                cout << contig << " " << position << endl;
            }
        }
        prev_line_last_char = line[line.size() - 1];
    }
 }
	/*
	Copyright 2019 Avinash Ramu

	Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

	The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
	*/

	//Takes a kmer and fasta as input and lists all positions
	//within the fasta for that kmer.
	//Example usage ./a.out hg38.fa AT
	#include <iostream>
	#include <fstream>
	#include <sstream>

	using namespace std;

	int main(int argc, char* argv[]) {
	if (argc != 3) {
	cerr << "Example usage ./a.out hg38.fa AT";
	return 1;
	}
	string kmer = argv[2];

	// Read the FASTA
	ifstream fasta_fh(argv[1]);
	std::string line, contig;
	long position;
	char prev_line_last_char; // STore the last character of previous line
	int line_number = 0;
	while(std::getline(fasta_fh, line).good()) {
	if (line[0] == '>') {
	istringstream iss(line.substr(1));
	iss >> contig; // Get the chromosome name
	prev_line_last_char = '0';
	position = 0;
	continue;
	}
	for (std::string::size_type i = 0; i < line.size(); i++) {
	position += 1;
	if(i == 0 && prev_line_last_char != '0') { //CHeck concatenation with prev line
	string first;
	first += prev_line_last_char;
	first += line[0];
	if(first == kmer) {
	cout << contig << " " << position << endl;
	}
	}
	string twomer; //Compare consecutive characters
	twomer += line[i];
	twomer += line[i+1];
	if(twomer == kmer) { // Check if the 2mer is what we want
	cout << contig << " " << position << endl;
	}
	}
	prev_line_last_char = line[line.size() - 1];
	}
	}