const string off_targets_by_seq(const MongooseRequest& request) {
ots_data_t result;
string sequence;
string species;
string pam_right_param;
vector<uint64_t> matches;
bool pam_right;
string jason_result;
request.getVar("seq", sequence);
request.getVar("species", species);
request.getVar("pam_right", pam_right_param);
pam_right = false;
if ( pam_right_param == "true" ) {
pam_right = true;
}
else if ( pam_right_param == "false" ) {
pam_right = false;
}
else {
throw runtime_error("pam_right must be the string true or false");
}
result = get_util(species)->off_targets_by_seq( sequence, pam_right);
jason_result = util::to_string(result);
return jason_result;
}
const string id_json(const MongooseRequest& request) {
vector<string> seqs;
string ids_text, species;
request.getVar("ids", ids_text);
request.getVar("species", species);
if ( ids_text.empty() )
throw runtime_error("Please provide ids as a comma separated string");
if ( species.empty() )
throw runtime_error("Please provide a species");
util::lc(species);
vector<string> ids = util::split(ids_text);
//should maybe change this to return an object of { id: sequence }
for ( vector<string>::size_type i = 0; i < ids.size(); i++ ) {
cerr << "Getting sequence for " << ids[i] << " (" << species << ")\n";
unsigned long long id;
try {
id = stoull(ids[i]);
}
catch (const invalid_argument &e) {
throw runtime_error("id " + ids[i] + " not an integer");
}
seqs.push_back( "'" + get_util(species)->get_crispr(id) + "'" );
}
return util::to_json_array(seqs);
}
const string find_off_targets(const MongooseRequest& request) {
string species;
string result = "{";
vector<uint64_t> ids_all;
string ids_text;
request.getVar("ids", ids_text);
request.getVar("species", species);
if ( ids_text.empty() )
throw runtime_error("Please provide ids");
if ( species.empty() )
throw runtime_error("Please provide a species");
util::lc(species);
vector<string> ids = util::split(ids_text);
for ( vector<string>::size_type i = 0; i < ids.size(); i++ ) {
unsigned long long id;
try {
id = stoull(ids[i]);
}
catch (const invalid_argument &e) {
throw runtime_error("id " + ids[i] + " not an integer");
}
ids_all.push_back(id);
}
vector<ots_data_t> offs = get_util(species)->find_off_targets(ids_all, true);
for ( uint i = 0; i < offs.size(); ++i ) {
if ( i > 0 ) result += ",";
//we use my to_string here as its a struct we want a string of
result += "\"" + to_string(offs[i].id) + "\":" + util::to_string(offs[i]);
}
result += "}";
//result = "Got data for " + to_string(offs.size()) + " crisprs";
return result;
}
//wrap a json string in jsonp. return true if it was jsonp
bool handle_jsonp(const MongooseRequest& request, string& result) {
string callback;
request.getVar("callback", callback);
if ( callback.empty() ) return false;
callback += "(";
result.insert(0, callback);
result += ");";
return true;
}
void get_matches(const MongooseRequest& request, vector<uint64_t>& matches) {
string seq;
string pam_right_str;
string species;
request.getVar("seq", seq);
request.getVar("pam_right", pam_right_str);
request.getVar("species", species);
//make species lowercase
util::lc( species );
//default pam_right is 2, which means don't consider the pam
if ( pam_right_str.size() == 0 ) pam_right_str = "2";
if ( seq.empty() )
throw runtime_error("Please provide a sequence");
if ( seq.size() != 20 )
throw runtime_error("Sequence must be 20 bases long");
if ( pam_right_str.empty() )
throw runtime_error("Please specify pam right");
int pam_right = atoi( pam_right_str.c_str() );
if ( ! ( pam_right == 0 || pam_right == 1 || pam_right == 2 ) )
throw runtime_error("pam_right must be 0, 1 or 2");
if ( species.empty() )
throw runtime_error("Please specify a species");
cerr << "Searching for " << seq << ", pam_right is " << pam_right << endl;
get_util(species)->search_by_seq( seq, pam_right, matches );
}