// ----------------------------------------
// ---------- mussa_class.cc -----------
// ----------------------------------------
+#include <boost/filesystem/operations.hpp>
+#include <boost/filesystem/fstream.hpp>
+namespace fs = boost::filesystem;
-#include <fstream>
#include <iostream>
#include <sstream>
return the_seqs;
}
-void Mussa::load_sequence(string seq_file, string annot_file, int fasta_index,
- int sub_seq_start, int sub_seq_end)
+void Mussa::load_sequence(fs::path seq_file, fs::path annot_file,
+ int fasta_index, int sub_seq_start, int sub_seq_end)
{
Sequence aseq;
aseq.load_fasta(seq_file, fasta_index, sub_seq_start, sub_seq_end);
- if (annot_file.size() > 0) {
+ if ( not annot_file.empty() ) {
aseq.load_annot(annot_file, sub_seq_start, sub_seq_end);
}
the_seqs.push_back(aseq);
}
void
-Mussa::load_mupa_file(string para_file_path)
+Mussa::load_mupa_file(fs::path para_file_path)
{
- string file_path_base;
- ifstream para_file;
+ fs::ifstream para_file;
string file_data_line;
- string param, value, annot_file;
+ string param, value;
+ fs::path annot_file;
int split_index, fasta_index;
int sub_seq_start, sub_seq_end;
bool seq_params, did_seq;
// initialize values
clear();
- para_file.open(para_file_path.c_str(), ios::in);
-
// if file was opened, read the parameter values
- if (para_file)
+ if (fs::exists(para_file_path))
{
- // need to find the path to the .mupa file
- parsing_path = true;
- dir_index = 0;
- while (parsing_path)
- {
- new_index = (para_file_path.substr(dir_index)).find("/");
- if (new_index != string::npos)
- dir_index += new_index + 1;
- else
- parsing_path = false;
- }
+ para_file.open(para_file_path, ios::in);
- file_path_base = para_file_path.substr(0,dir_index);
+ // what directory is the mupa file in?
+ fs::path file_path_base = para_file_path.branch_path();
// setup loop by getting file's first line
getline(para_file,file_data_line);
threshold = atoi(value.c_str());
else if (param == "SEQUENCE")
{
- string seq_file = file_path_base + value;
+ fs::path seq_file = file_path_base / value;
//cout << "seq_file_name " << seq_files.back() << endl;
fasta_index = 1;
annot_file = "";
if (param == "FASTA_INDEX")
fasta_index = atoi(value.c_str());
else if (param == "ANNOTATION")
- annot_file = file_path_base + value;
+ annot_file = file_path_base / value;
else if (param == "SEQ_START")
sub_seq_start = atoi(value.c_str());
else if (param == "SEQ_END")
// no file was loaded, signal error
else
{
- throw mussa_load_error("Config File: " + para_file_path + " not found");
+ throw mussa_load_error("Config File: " + para_file_path.string() + " not found");
}
}
void
Mussa::save()
{
- string save_name, save_path, create_dir_cmd, flp_filepath;
- fstream save_file;
+ string save_name;
+ fs::path flp_filepath;
+ fs::fstream save_file;
ostringstream append_info;
int dir_create_status;
+ if (not analysis_name.empty()) {
+ // not sure why, but gotta close file each time since can't pass
+ // file streams
+ save_name = analysis_name;
- // not sure why, but gotta close file each time since can't pass file streams
-
- save_name = analysis_name;
-
- // gotta do bit with adding win & thres if to be appended
- if (win_append)
- {
- append_info.str("");
- append_info << "_w" << window;
- save_name += append_info.str();
- }
-
- if (thres_append)
- {
- append_info.str("");
- append_info << "_t" << threshold;
- save_name += append_info.str();
- }
+ // gotta do bit with adding win & thres if to be appended
+ if (win_append)
+ {
+ append_info.str("");
+ append_info << "_w" << window;
+ save_name += append_info.str();
+ }
-//#include <stdlib.h>
- // ******* use appropriate for os ------- 1 of 4
- // the additions for osX make it more sane where it saves the analysis
- // will come up with a cleaner sol'n later...
- create_dir_cmd = "mkdir " + save_name; //linux
- //create_dir_cmd = "mkdir " + file_path_base + save_name; //osX
+ if (thres_append)
+ {
+ append_info.str("");
+ append_info << "_t" << threshold;
+ save_name += append_info.str();
+ }
+ fs::path save_path( save_name);
- dir_create_status = system( (const char*) create_dir_cmd.c_str());
- //cout << "action: " << dir_create_status << endl;
+ if (not fs::exists(save_path)) {
+ fs::create_directory(save_path);
+ }
+ // save sequence and annots to a special mussa file
+ save_file.open(save_path / (save_name+".museq"), ios::out);
+ save_file << "<Mussa_Sequence>" << endl;
- // save sequence and annots to a special mussa file
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ {
+ the_seqs[i].save(save_file);
+ }
- // ******** use appropriate for OS ---------- 2 of 4
- save_path = save_name + "/" + save_name + ".museq"; //linux
- //save_path = file_path_base + save_name + "/" + save_name + ".museq"; //osX
+ save_file << "</Mussa_Sequence>" << endl;
+ save_file.close();
- save_file.open(save_path.c_str(), ios::out);
- save_file << "<Mussa_Sequence>" << endl;
- //save_file.close();
+ // save nway paths to its mussa save file
+ the_paths.save(save_path / (save_name + ".muway"));
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- {
- the_seqs[i].save(save_file);
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
+ {
+ append_info.str("");
+ append_info << "_sp_" << i << "v" << i2;
+ all_comps[i][i2].save(save_path/(save_name+append_info.str()+".flp"));
+ }
}
-
- //save_file.open(save_path.c_str(), ios::app);
- save_file << "</Mussa_Sequence>" << endl;
- save_file.close();
-
- // save nway paths to its mussa save file
-
- // ******** use appropriate for OS -------- 3 of 4
- save_path = save_name + "/" + save_name + ".muway"; //linux
- //save_path = file_path_base + save_name + "/" + save_name + ".muway"; //os X
- the_paths.save(save_path);
-
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
- {
- append_info.str("");
- append_info << "_sp_" << i << "v" << i2;
- // ******** use appropriate for OS --------- 4 of 4
- //linux
- save_path = save_name + "/" + save_name + append_info.str() + ".flp";
- //osX
- //save_path = file_path_base + save_name + "/" + save_name + append_info.str() + ".flp";
- all_comps[i][i2].save(save_path);
- }
}
void
-Mussa::save_muway(string save_path)
+Mussa::save_muway(fs::path save_path)
{
the_paths.save(save_path);
}
void
-Mussa::load(string ana_file)
+Mussa::load(fs::path ana_file)
{
int i, i2;
- string::size_type start_index, end_index;
- string file_path_base, a_file_path, ana_path;
+ fs::path file_path_base;
+ fs::path a_file_path;
+ fs::path ana_path(ana_file);
bool parsing_path;
Sequence tmp_seq;
string err_msg;
vector<FLPs> empty_FLP_vector;
FLPs dummy_comp;
- //cout << "ana_file name " << ana_file << endl;
- ana_path = ana_file;
- parsing_path = true;
- end_index = ana_path.size()-1;
- if (ana_path[end_index] == '/') {
- --end_index;
- }
- start_index = ana_path.rfind('/', end_index);
- if (start_index == string::npos) {
- // no / to be found
- start_index = 0;
- } else {
- // skip the / we found
- ++start_index;
- }
- analysis_name = ana_path.substr(start_index, end_index-start_index+1);
+ //cout << "ana_file name " << ana_file.string() << endl;
+ analysis_name = ana_path.leaf();
//cout << " ana_name " << analysis_name << endl;
- file_path_base = ana_path.substr(0, start_index) + analysis_name
- + "/" + analysis_name;
- a_file_path = file_path_base + ".muway";
- //cout << " loading museq: " << a_file_path << endl;
+ file_path_base = ana_path.branch_path() / analysis_name;
+ a_file_path = file_path_base / (analysis_name + ".muway");
+ //cout << " loading museq: " << a_file_path.string() << endl;
the_paths.load(a_file_path);
// perhaps this could be more elegent, but at least this'll let
// us know what our threshold and window sizes were when we load a muway
int seq_num = the_paths.sequence_count();
- a_file_path = file_path_base + ".museq";
+ a_file_path = file_path_base / (analysis_name + ".museq");
// this is a bit of a hack due to C++ not acting like it should with files
for (i = 1; i <= seq_num; i++)
{
tmp_seq.clear();
- //cout << "mussa_class: loading museq frag... " << a_file_path << endl;
+ //cout << "mussa_class: loading museq frag... " << a_file_path.string() << endl;
tmp_seq.load_museq(a_file_path, i);
the_seqs.push_back(tmp_seq);
}
for(i2 = i+1; i2 < seq_num; i2++)
{
append_info.str("");
- append_info << "_sp_" << i << "v" << i2;
+ append_info << analysis_name << "_sp_" << i << "v" << i2 << ".flp";
//cout << append_info.str() << endl;
- a_file_path = file_path_base + append_info.str() + ".flp";
+ a_file_path = file_path_base / append_info.str();
+ //cout << "path " << a_file_path.string() << endl;
all_comps[i][i2].load(a_file_path);
//cout << "real size = " << all_comps[i][i2].size() << endl;
}
void
Mussa::save_old()
{
- fstream save_file;
+ fs::fstream save_file;
- save_file.open(analysis_name.c_str(), ios::out);
+ save_file.open(analysis_name, ios::out);
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
save_file << the_seqs[i].get_seq() << endl;
update_sequences_motifs();
}
-void Mussa::load_motifs(string filename)
+void Mussa::load_motifs(fs::path filename)
{
- ifstream f;
- f.open(filename.c_str(), ifstream::in);
+ fs::ifstream f;
+ f.open(filename, ifstream::in);
load_motifs(f);
}
projects / mussa.git / blobdiff