diff gene_fraction/src/Fasta.cpp @ 0:f95150c37d38 draft default tip

planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/Fasta.cpp	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,39 @@
+#include "Fasta.h"
+#include "args.h"
+
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <string>
+
+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) {
+		usage();
+		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);
+}
+
+
+
+
+
+