mer... j'ai oublié le make install ... c'est pas la peine ? J'ai supprimé tous les dossiers de cisortho et opt et retelechargé opt pour reprendre a 0. Il est quand meme resté installé ?
#include <iostream>
#include <sstream>
#include "opt.h"
#include "index_trie.h"
#include "dnacol.h"
#include "dna_scanning.h"
#include "dnastats.h"
#include "dna.h"
#include "litestream.h"
#include <unistd.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>
using std::cerr;
using std::cout;
using std::endl;
using std::string;
int MinTreeDepth = 6;
int MaxTreeDepth = 50;
int MaxSuffixLoad = 2;
int PrefixLength = 2;
int ChunkSize = 100000;
char *OutfilePrefix = NULL;
char *SinglePrefix = NULL;
char *FolderPrefix = NULL;
char * DataDirectory = const_cast<char *>(".");
int n_DNA, n_Species;
char **DNA, **Species;
int GenomeIndex(int argc, char const** argv){
if (OutfilePrefix == NULL){
cerr<<"Please provide an output file prefix (option -o)"<<endl;
exit(53);
}
std::ostringstream TreeTempDir;
std::ostringstream PosTempDir;
if (FolderPrefix == NULL){
PosTempDir<<getpid()<<"_gpos";
TreeTempDir<<getpid()<<"_itrie";
}
else {
PosTempDir<<FolderPrefix<<"_gpos";
TreeTempDir<<FolderPrefix<<"_itrie";
}
//parse dna from SequenceFile, build a dna_collection from it
if (n_Species != n_DNA) {
cerr<<"You must have the same number of species names as genomic sequence files."<<endl;
exit(53);
}
std::vector<string> sSpecies(n_Species);
std::string sDataDirectory(DataDirectory);
for (int g=0; g < n_Species; g++) sSpecies[g] = Species[g];
cis::dna_collection dnac;
for (int g=0; g < n_DNA; g++){
try {
std::cout<<"Parsing "<<DNA[g]<<" genomic sequence file..."<<std::endl;
dnac.add(sSpecies[g], sDataDirectory, DNA[g]);
}
catch (string &msg){ cerr<<msg<<endl; return 2; }
}
dnac.calc_offsets();
dnac.open_dnas();
mkdir(TreeTempDir.str().c_str(), 0755);
mkdir(PosTempDir.str().c_str(), 0755);
DIR * treedir = opendir(TreeTempDir.str().c_str());
DIR * posdir = opendir(PosTempDir.str().c_str());
std::ofstream treefile, posfile;
std::ifstream tree_bufbase;
litestream tree_bufstream(tree_bufbase, ChunkSize);
// bfs::path treedir(TreeTempDir.str());
// bfs::path posdir(PosTempDir.str());
// bfs::create_directory(treedir);
// bfs::create_directory(posdir);
index_trie::set_max_suffix_load(MaxSuffixLoad);
index_trie * root = new index_trie();
cout<<"Scanning all dna for prefixes...";
cout.flush();
std::set<cis::dnastring> Prefixes, ptmp;
std::set<cis::dnastring>::iterator prefix_iter;
if (FolderPrefix != NULL){
dirent * current_file;
while ((current_file = readdir(treedir)) != NULL){
// bfs::directory_iterator end_itr; // default construction yields past-the-end
// for (bfs::directory_iterator itr(treedir); itr != end_itr; ++itr){
string prefix = current_file->d_name;
//string prefix = itr->leaf();
cis::dnastring dprefix = cis::ToDNAString(prefix);
Prefixes.insert(dprefix);
}
cis::dnastring pfx;
for (prefix_iter = Prefixes.begin();
prefix_iter != Prefixes.end(); ++prefix_iter){
pfx = *prefix_iter;
string spfx = cis::FromDNAString(pfx);
string treepath = TreeTempDir.str() + spfx;
string pospath = PosTempDir.str() + spfx;
tree_bufstream.open(treepath.c_str());
if (! tree_bufstream.good()){
cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
exit(50);
}
node_info subroot = readNode(tree_bufstream);
root->insertfile(pfx.c_str(), pfx.size(),
treepath, subroot.subtree_size,
pospath, subroot.suffix_count);
tree_bufstream.close();
}
}
else {
for (cis::DNAS::iterator dna_it = dnac.begin();
dna_it != dnac.end(); ++dna_it){
ptmp = dnastats::Spectrum(*(*dna_it), PrefixLength, ChunkSize);
Prefixes.insert(ptmp.begin(), ptmp.end());
}
cout<<"found "<<Prefixes.size()<<" prefixes."<<endl;
cis::dnastring pfx;
for (prefix_iter = Prefixes.begin();
prefix_iter != Prefixes.end(); ++prefix_iter){
pfx = *prefix_iter;
index_trie * subroot = new index_trie();
subroot->build_subtree(pfx, dnac, MinTreeDepth, MaxTreeDepth, ChunkSize);
subroot->push();
cis::NUC lastNuc = *pfx.rbegin();
if (! subroot->empty()){
subroot->count();
string spfx = cis::FromDNAString(pfx);
string treepath = TreeTempDir.str() + string("/") + spfx;
string pospath = PosTempDir.str() + string("/") + spfx;
treefile.open(treepath.c_str(), std::ios::out | std::ios::binary);
//treefile.open(treedir / spfx, std::ios::out | std::ios::binary);
if (! treefile){
cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
exit(50);
}
posfile.open(pospath.c_str(), std::ios::out | std::ios::binary);
//posfile.open(posdir / spfx, std::ios::out | std::ios::binary);
if (! posfile){
cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
exit(50);
}
cout<<"Writing subtree with prefix "<<spfx<<", "
<<subroot->nbytes<<" bytes, "
<<subroot->nsuffixes<<" patterns...";
cout.flush();
subroot->write(lastNuc, treefile, posfile);
treefile.close();
posfile.close();
root->insertfile(pfx.c_str(), pfx.size(),
treepath, subroot->nbytes,
pospath, subroot->nsuffixes);
// root->insertfile(pfx.c_str(), pfx.size(),
// treedir / spfx, subroot->nbytes,
// posdir / spfx, subroot->nsuffixes);
cout<<"done."<<endl;
//return 0;
}
delete subroot; //memory
}
}
string tree(OutfilePrefix); tree += ".itrie";
treefile.open(tree.c_str(), std::ios::out | std::ios::binary);
string pos(OutfilePrefix); pos += ".gpos";
posfile.open(pos.c_str(), std::ios::out | std::ios::binary);
//return 0;
root->push();
root->count();
root->write(cis::X, treefile, posfile);
cout<<"Wrote "<<root->nbytes<<" bytes and "
<<root->nsuffixes<<" patterns."<<endl;
delete root;
treefile.close();
posfile.close();
string dnasrc(OutfilePrefix); dnasrc += ".dnas";
std::ofstream dnafile;
dnafile.open(dnasrc.c_str());
for (cis::DNAS::iterator dna_it = dnac.begin();
dna_it != dnac.end(); ++dna_it)
dnafile<<*(*dna_it)<<endl;
dnafile.close();
//delete all files in treedir, posdir
cout<<"Removing all files in "
<<TreeTempDir.str().c_str()
<<" and "<<PosTempDir.str().c_str()<<"."<<endl;
dirent * current_file;
while ((current_file = readdir(treedir)) != NULL) {
cout<<"Would be unlinking "<<current_file->d_name<<endl;
//unlink(current_file->d_name);
}
rmdir(TreeTempDir.str().c_str());
while ((current_file = readdir(posdir)) != NULL) {
cout<<"Would be unlinking "<<current_file->d_name<<endl;
//unlink(current_file->d_name);
}
rmdir(PosTempDir.str().c_str());
// bfs::remove_all(treedir);
// bfs::remove_all(posdir);
return 0;
}
int main(int argc, char const**argv){
OptRegister(&MinTreeDepth,OPT_INT, 'x', "min-tree-depth","minimum pattern length to search.");
OptRegister(&MaxTreeDepth,OPT_INT, 'y', "max-tree-depth","maximum depth of the index tree.");
OptRegister(&PrefixLength,OPT_INT, 'p', "prefix-length","length of prefix (3 is good) for splitting the subtree building.");
OptRegister(&MaxSuffixLoad,OPT_INT, 'l', "max-suffix-load","maximum number of suffixes at a leaf before pushing further");
OptRegister(&ChunkSize,OPT_INT, 'c', "chunk-size","size of reading a chunk of DNA sequence for scanning");
optrega_array(&n_Species, &Species, OPT_STRING,'n', "species-names","species names (comma-separated)");
optrega_array(&n_DNA, &DNA, OPT_STRING, 's', "sequence-files","sequence files (comma-separated)");
OptRegister(&DataDirectory, OPT_STRING, 't', "dna-directory", "directory containing 'sequence-files'");
OptRegister(&OutfilePrefix,OPT_STRING, 'o', "outfile-prefix","prefix on output files with extensions 'gpos', 'itree', and 'dnas'");
OptRegister(&SinglePrefix,OPT_STRING, 'f', "single-prefix","for testing");
OptRegister(&FolderPrefix,OPT_STRING, 'd', "folder-prefix","for partial runs");
optMain(GenomeIndex);
if (argc==1){
char const** myargv;
char const* mybuf[2];
mybuf[0]=argv[0];
mybuf[1]="$";
myargv=mybuf;
int myargc=2;
cout<<endl<<endl
<<"Build a tree and genome position index file from a sequence file"<<endl
<<"for fast, ungapped pattern searching."<<endl;
opt(&myargc,&myargv);
}
else opt(&argc,&argv);
return GenomeIndex(argc,argv);
}
