view snp_caller/src/Fasta.cpp @ 0:0fd352f62446 draft default tip

planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty

#include "Fasta.h"

#include <string>
#include <fstream>
#include <vector>
#include <iostream>


Fasta::Fasta(std::string amr_fp) : _amr_fp(amr_fp) {}

void Fasta::read_fasta(const std::string &amr_fp) {
        std::ifstream in(amr_fp.c_str());
        if(!in) {
                std::cerr << "Could not open fasta file " << amr_fp << std::endl;
                exit(EXIT_FAILURE);
        }

        std::string gene_id, gene, line;
        while(std::getline(in, line)) {
                std::size_t gene_idx = line.find(" ");

                if(gene_idx != std::string::npos)
                        gene_id = line.substr(1, gene_idx-1);
                else
                        gene_id = line.substr(1, line.length());

                std::getline(in, gene);
                records.push_back(FastaRecord(gene_id, gene));
        }
        in.close();

        FastaRecord::sort_by_gene_id(records);
}