/* Dict::initialize: returns true if the map is ready to be searched, false otherwise.
*/
bool Dict::initialize()
{
ifstream dictfile(dictfileName.c_str(), ifstream::in);
if (dictfile.good())
{
loadDict();
}
else
{
cout << "Dictionary file not present. Creating new file. This may take some time..." << endl;
createDict();
}
if (USE_BLACKLIST)
{
try
{
blacklistfile.open(blacklistfileName.c_str(), ifstream::in);
// cout << "Loading Blacklist..." << endl;
if (blacklistfile.good())
loadBlacklist();
}
catch (ifstream::failure e)
{
cout << "Warning: Blacklist file not present!" << endl;
}
}
return true;
}
void FSWSAssetBlacklist::init()
{
mBlacklistFileName = gDirUtilp->getExpandedFilename(LL_PATH_PER_SL_ACCOUNT, "asset_blacklist.xml");
loadBlacklist();
}
int main(int argc, char *argv[])
{
if (argc != 3)
{
std::cout << std::endl
<< "Filter peptides is used to filter pep.xml files from blacklisted peptides after the search has been performed. For example shared peptides between two species or known containments."
<< std::endl;
std::cerr << "Usage: filterPeptides [file.pep.xml] [blacklist]" << std::endl;
exit(1);
}
//Load the blacklist in our hashmap for fast acces
std::unordered_set<std::string> blacklistSet(loadBlacklist(argv[2]));
std::cout << "Blacklist (" << argv[2] << ") contains " << blacklistSet.size() << " peptides" << std::endl;
std::string inFile(argv[1]);
std::string extension(".pep.xml");
std::string outFile(inFile.substr(0, inFile.length() - extension.length()));
outFile.append(".filtered.pep.xml");
std::ofstream outputStream(outFile, std::ofstream::out | std::ofstream::trunc);
pugi::xml_document doc;
pugi::xml_parse_result result = doc.load_file(argv[1]);
if (result)
{
pugi::xml_object_range<pugi::xml_named_node_iterator> spectrumQueries =
doc.child("msms_pipeline_analysis").child("msms_run_summary").children("spectrum_query");
std::cout << "pugixml: [" << argv[1] << "] parsed without errors, total spectrum queries: "
<< std::distance(spectrumQueries.begin(), spectrumQueries.end()) << "\n";
}
else
{
std::cout << "pugixml: [" << argv[1] << "] parsed with errors\n";
std::cout << "Error description: " << result.description() << "\n";
std::cout << "Error offset: " << result.offset;
exit(1);
}
unsigned totalDeleted = 0;
unsigned totalPeptides = 0;
//Containers to store our nodes we need to delete afterwards
std::vector<pugi::xml_node> spectrumToDelete;
std::vector<pugi::xml_node> searchhitToDelete;
//Initialize the searchhitNodes counter
unsigned searchhitNodes = 0;
for (pugi::xml_node spectrum : doc.child("msms_pipeline_analysis").child("msms_run_summary").children(
"spectrum_query"))
{
//Temp variable for easier acces
pugi::xml_object_range<pugi::xml_named_node_iterator> search_resultNodes =
spectrum.child("search_result").children("search_hit");
for (pugi::xml_node search_hit : search_resultNodes)
{
if (blacklistSet.find(search_hit.attribute("peptide").as_string()) != blacklistSet.end())
{
//notify the user of our node deletion
std::cout << "Deleting from spectrum '" << spectrum.attribute("spectrum").as_string();
std::cout << "' peptide hit '" << search_hit.attribute("peptide").as_string();
std::cout << "' (rank:" << search_hit.attribute("hit_rank").as_uint() << ")" << "\n";
searchhitToDelete.push_back(search_hit);
}
totalPeptides++;
}
if (searchhitToDelete.size() == 0)
{
//Short circuit and skip expensive deletion of nodes
continue;
}
//Count the total amount of nodes
searchhitNodes = std::distance(search_resultNodes.begin(), search_resultNodes.end());
totalDeleted+=searchhitToDelete.size();
if ((searchhitNodes - searchhitToDelete.size()) == 0)
{
//if the results are empty, delete the whole spectrum with it's query entries
spectrumToDelete.push_back(spectrum);
}
else
{
//Remove the required nodes
for (pugi::xml_node &search_hit : searchhitToDelete)
{
spectrum.child("search_result").remove_child(search_hit);
}
//TODO re-score the hit ranks of the other nodes
}
searchhitToDelete.clear();
}
//Clean up empty spectrum nodes
for (pugi::xml_node &spectrum : spectrumToDelete)
{
doc.child("msms_pipeline_analysis").child("msms_run_summary").remove_child(spectrum);
}
//Pritn final results to the user
std::cout << "Total peptides deleted: " << totalDeleted << " of " << totalPeptides << " peptide hits and removed "
<< spectrumToDelete.size() << " empty spectrum_query results." << std::endl;
std::cout << "Saving result: " << (doc.save_file(outFile.c_str(), "") ? outFile.c_str() : "failed") << std::endl
<< std::endl;
}