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patch to htgt/CRISPR-Analyser
diff --git a/src/crisprutil.cpp b/src/crisprutil.cpp
index 91d9b4c..0480e27 100644
--- a/src/crisprutil.cpp
+++ b/src/crisprutil.cpp
@@ -44,6 +44,10 @@ void CrisprUtil::_populate_cmap() {
string CrisprUtil::get_crispr(uint64_t id) {
return util::bits_to_string( get_crispr_int(id), crispr_data.seq_length );
}
+// 2014-9-9 : id with offset need to be correct
+string CrisprUtil::get_offset_crispr(uint64_t id) {
+ return util::bits_to_string( get_crispr_int(id - crispr_data.offset), crispr_data.seq_length );
+}
uint64_t CrisprUtil::get_crispr_int(uint64_t id) {
//make sure load_binary has been called
diff --git a/src/crisprutil.h b/src/crisprutil.h
index aaf1498..939c99e 100644
--- a/src/crisprutil.h
+++ b/src/crisprutil.h
@@ -55,6 +55,7 @@ class CrisprUtil {
uint8_t cmap[256];
void load_binary(const std::string & outfile);
std::string get_crispr(uint64_t id);
+ std::string get_offset_crispr(uint64_t id);
uint64_t get_crispr_int(uint64_t id);
uint64_t num_seqs();
uint64_t seq_length();
diff --git a/src/ots_server.cpp b/src/ots_server.cpp
index 12f6d93..6a194e4 100644
--- a/src/ots_server.cpp
+++ b/src/ots_server.cpp
@@ -146,6 +146,10 @@ protected:
result = search_json(request);
res = true;
}
+ else if ( uri == string("/api/id") ) {
+ result = id_json(request);
+ res = true;
+ }
else if ( uri == string("/api/off_targets") ) {
result = find_off_targets(request);
res = true;
@@ -193,6 +197,8 @@ protected:
response.setConnectionAlive(false);
response.setCacheDisabled();
response.setContentType(content_type);
+ response.setHeaderValue("Access-Control-Allow-Origin", "*");
+ response.setHeaderValue("Cache-Control", "no-cache, must-revalidate");
response.addContent(result);
response.write();
}
@@ -260,6 +266,28 @@ protected:
return util::to_json_array(matches);
}
+ const string id_json(const MongooseRequest& request) {
+ vector<string> seqs;
+ string ids_text;
+ request.getVar("ids", ids_text);
+ string species;
+ 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 ( uint64_t i = 0; i < ids.size(); i++ ) {
+ seqs.push_back( "'" + get_util(species)->get_offset_crispr( stoull(ids[i]) ) + "'" );
+ }
+
+ return util::to_json_array(seqs);
+ }
+
const string find_off_targets(const MongooseRequest& request) {
string species;
string result = "{";
@@ -320,7 +348,7 @@ protected:
int usage() {
fprintf(stderr, "\n");
fprintf(stderr, "Program: ots_server\n");
- fprintf(stderr, "Contact: Alex Hodgkins <ah19@sanger.ac.uk>\n");
+ fprintf(stderr, "Contact: Alex Hodgkins <ah19@sanger.ac.uk>, Liang Cai\n");
fprintf(stderr, "Description: A server version of the crispr_analyser that responds to JSON requests\n");
fprintf(stderr, "\n");
fprintf(stderr, "Usage: ots_server [options]\n");
@@ -329,7 +357,8 @@ int usage() {
fprintf(stderr, " -p INT The port to run the server on\n");
fprintf(stderr, " -l FILE The file containing the human CRISPR index\n");
fprintf(stderr, " -m FILE The file containing the mouse CRISPR index\n");
- fprintf(stderr, " -s Load the default mouse/crispr indexes (sanger only)\n");
+ fprintf(stderr, " -g FILE The file containing the dog CRISPR index\n");
+ fprintf(stderr, " -s Load the default mouse/crispr indexes (fb.actin only)\n");
fprintf(stderr, " -d Daemon mode\n");
fprintf(stderr, "\n");
@@ -342,14 +371,15 @@ int main(int argc, char * argv[]) {
bool default_opts = false;
bool daemon = false;
- string human_index, mouse_index;
+ string human_index, mouse_index, dog_index;
int c = -1;
- while ( (c = getopt(argc, argv, "t:p:l:m:sd")) != -1 ) {
+ while ( (c = getopt(argc, argv, "t:p:l:m:g:sd")) != -1 ) {
switch ( c ) {
case 't': num_threads = optarg; break;
case 'p': port = optarg; break;
case 'l': human_index = optarg; break;
case 'm': mouse_index = optarg; break;
+ case 'g': dog_index = optarg; break;
case 's': default_opts = true; break;
case 'd': daemon = true; break;
case '?': return usage();
@@ -357,12 +387,13 @@ int main(int argc, char * argv[]) {
}
if ( default_opts ) {
- human_index = "/lustre/scratch109/sanger/team87/crispr_indexes/GRCh37_index.bin";
- mouse_index = "/lustre/scratch109/sanger/team87/crispr_indexes/GRCm38_index.bin";
+ human_index = "/home/liang/crisprs_human.bin";
+ mouse_index = "/home/liang/crisprs_mouse.bin";
+ dog_index = "/home/liang/crisprs_cf3.bin";
}
else {
- if ( human_index.empty() && mouse_index.empty() ) {
- cerr << "You must specify at least 1 index to load, or use -s to use the default indexes in /lustre" << endl;
+ if ( human_index.empty() && mouse_index.empty() && dog_index.empty() ) {
+ cerr << "You must specify at least 1 index to load, or use -s to use the default indexes" << endl;
return usage();
}
}
@@ -397,6 +428,7 @@ int main(int argc, char * argv[]) {
if ( ! human_index.empty() ) server.load_index("human", human_index);
if ( ! mouse_index.empty() ) server.load_index("mouse", mouse_index);
+ if ( ! dog_index.empty() ) server.load_index("dog", dog_index);
server.setOption("document_root", "html");
server.setOption("listening_ports", port);
@coronin
Owner
coronin commented Sep 8, 2014

ots_server has jsonp support
the following is not required
Access-Control-Allow-Origin "*"

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