FASTA reader written in C++? - c++

Question

Let me start off by stating that I am a beginner in C++. Anyways, the FASTA format goes as follows:
Any line starting with a '>' indicates the name/id of the gene sequence right below it. There is a gene sequence right below the id. This gene sequence can be 1 or multiple lines.
So... what I want to do is print: id << " : " << gene_sequence << endl;
Here is my code:
#include <iostream>
#include <fstream>
int main(int argc, char **argv) {
if (argc < 2) {
std::cerr << " Wrong format: " << argv[0] << " [infile] " << std::endl;
return -1;
}
std::ifstream input(argv[1]);
if (!input.good()) {
std::cerr << "Error opening: " << argv[1] << " . You have failed." << std::endl;
return -1;
}
std::string line, id, DNA_sequence;
while (std::getline(input, line).good()) {
if (line[0] == '>') {
id = line.substr(1);
std::cout << id << " : " << DNA_sequence << std::endl;
DNA_sequence.clear();
}
else if (line[0] != '>'){
DNA_sequence += line;
}
}
}
For the second argument inputted into the command line, here is the content of my file:
>DNA_1
GATTACA
>DNA_2
TAGACCA
TAGACCA
>DNA_3
ATAC
>DNA_4
AT
Please copy and paste into text file.
After this has been done, and the code has been executed, I want to point out the problem. The code skips inputting the sequence of DNA_1 into its correct respective place, and instead placing DNA_1 's sequence into DNA_2. The results get pushed forward 1 as a result. Any assistance or tips would be greatly appreciated?
As I've said before, I am new to C++. And the semantics are quite hard to learn compared to Python.

Answer 1

I see a few problems with your code.
First you loop on std::ifstream::good() which doesn't work because it won't allow for End Of File (which happens even after a good read).
Then you access line[0] without checking if the line is empty which could cause a seg-fault.
Next you output the "previous line" before you have even collected it.
Finally you don't output the final line because the loop terminates when it doesn't find another >.
I added comments to my corrections to your code:
#include <iostream>
#include <fstream>
int main(int argc, char **argv) {
if (argc < 2) {
std::cerr << " Wrong format: " << argv[0] << " [infile] " << std::endl;
return -1;
}
std::ifstream input(argv[1]);
if (!input.good()) {
std::cerr << "Error opening: " << argv[1] << " . You have failed." << std::endl;
return -1;
}
std::string line, id, DNA_sequence;
// Don't loop on good(), it doesn't allow for EOF!!
// while (std::getline(input, line).good()) {
while (std::getline(input, line)) {
// line may be empty so you *must* ignore blank lines
// or you have a crash waiting to happen with line[0]
if(line.empty())
continue;
if (line[0] == '>') {
// output previous line before overwriting id
// but ONLY if id actually contains something
if(!id.empty())
std::cout << id << " : " << DNA_sequence << std::endl;
id = line.substr(1);
DNA_sequence.clear();
}
else {// if (line[0] != '>'){ // not needed because implicit
DNA_sequence += line;
}
}
// output final entry
// but ONLY if id actually contains something
if(!id.empty())
std::cout << id << " : " << DNA_sequence << std::endl;
}
Output:
DNA_1 : GATTACA
DNA_2 : TAGACCATAGACCA
DNA_3 : ATAC
DNA_4 : AT

Answer 2

You're storing the new id before printing the old one:
id = line.substr(1);
std::cout << id << " : " << DNA_sequence << std::endl;
Swap the lines around for proper order. You probably also want to check if you have any id already present to skip the first entry.

Answer 3

working implementation is here
https://rosettacode.org/wiki/FASTA_format#C.2B.2B
only corrected
while( std::getline( input, line ).good() ){
to
while( std::getline( input, line ) ){
Code
#include <iostream>
#include <fstream>
int main( int argc, char **argv ){
if( argc <= 1 ){
std::cerr << "Usage: "<<argv[0]<<" [infile]" << std::endl;
return -1;
}
std::ifstream input(argv[1]);
if(!input.good()){
std::cerr << "Error opening '"<<argv[1]<<"'. Bailing out." << std::endl;
return -1;
}
std::string line, name, content;
while( std::getline( input, line ) ){
if( line.empty() || line[0] == '>' ){ // Identifier marker
if( !name.empty() ){ // Print out what we read from the last entry
std::cout << name << " : " << content << std::endl;
name.clear();
}
if( !line.empty() ){
name = line.substr(1);
}
content.clear();
} else if( !name.empty() ){
if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed
name.clear();
content.clear();
} else {
content += line;
}
}
}
if( !name.empty() ){ // Print out what we read from the last entry
std::cout << name << " : " << content << std::endl;
}
return 0;
}
input:
>Rosetta_Example_1
THERECANBENOSPACE
>Rosetta_Example_2
THERECANBESEVERAL
LINESBUTTHEYALLMUST
BECONCATENATED
output:
Rosetta_Example_1 : THERECANBENOSPACE
Rosetta_Example_2 : THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED