Added RLCSA index option

[SXSI/TextCollection.git] / incbwt / utils / extract_text.cpp

diff --git a/incbwt/utils/extract_text.cpp b/incbwt/utils/extract_text.cpp
new file mode 100644 (file)
index 0000000..1306579
--- /dev/null
+++ b/incbwt/utils/extract_text.cpp
@@ -0,0 +1,82 @@
+#include <cstdlib>
+#include <fstream>
+#include <iostream>
+
+#include "../misc/definitions.h"
+
+
+using namespace CSA;
+
+
+std::string gapChars = " =-_";
+
+void
+concatenateStrain(std::string &text, std::ifstream &file, usint strain)
+{
+  file.clear();
+  file.seekg(0, std::ios::beg);
+
+  std::string line;
+  while(!file.eof())
+  {
+    getline(file, line);
+    if(line.empty() || line[0] == '>') { continue; }
+    char t = toupper(line[strain * 2]);
+    if(gapChars.find(t) == std::string::npos) { text.push_back(t); }
+  }
+}
+
+
+int
+main(int argc, char** argv)
+{
+  std::cout << "Extracting concatenated text from alignment" << std::endl;
+  if(argc < 3)
+  {
+    std::cout << "Usage: extract_text alignment_file output_file" << std::endl;
+    return 1;
+  }
+
+  std::cout << "Alignment file: " << argv[1] << std::endl;
+  std::ifstream alignment_file(argv[1], std::ios_base::binary);
+  if(!alignment_file)
+  {
+    std::cerr << "Error opening alignment file!" << std::endl;
+    return 2;
+  }
+
+  std::cout << "Output file: " << argv[2] << std::endl;
+  std::ofstream output_file(argv[2], std::ios_base::binary);
+  if(!output_file)
+  {
+    std::cerr << "Error creating output file!" << std::endl;
+    return 3;
+  }
+  std::cout << std::endl;
+
+  std::string line;
+  std::getline(alignment_file, line); // Skipping header line.
+  std::getline(alignment_file, line);
+  usint strains = line.size() / 2 - 1;
+  std::cout << "Number of strains: " << strains << std::endl;
+
+  line.clear();
+  concatenateStrain(line, alignment_file, 0);
+  usint n = line.size();
+  std::cout << "Reference sequence length: " << n << std::endl;
+
+  for(usint i = 1; i <= strains; i++)
+  {
+    concatenateStrain(line, alignment_file, i);
+  }
+  usint N = line.size() + 1;
+  std::cout << "Total length: " << N << std::endl;
+
+  output_file.write(line.c_str(), N - 1);
+  char end = '\0';
+  output_file.write(&end, 1);
+
+  output_file.close();
+  alignment_file.close();
+  return 0;
+}