All-vs-All mode: select target, not query

bin/run_minimap2.sh

@@ -6,15 +6,12 @@ minimap_exec=$1
 nb_threads=$2
 fasta_t=$3
 fasta_q=$4
-query=$5
-target=$6
-paf=$7
-paf_raw=$8
-out_dir=$9
+paf=$5
+paf_raw=$6
 
 # Run minimap:
 
-if [ "$fasta_t" != "NONE" ]; then
+if [ "$fasta_q" != "NONE" ]; then
 
 echo "Running: ${minimap_exec} -t ${nb_threads} ${fasta_t} ${fasta_q} > ${paf_raw}"
 
@@ -22,9 +19,9 @@ ${minimap_exec} -t ${nb_threads} ${fasta_t} ${fasta_q} > ${paf_raw}
 
 else
 
-echo "Running: ${minimap_exec} -t ${nb_threads} -X ${fasta_q} ${fasta_q} > ${paf_raw}"
+echo "Running: ${minimap_exec} -t ${nb_threads} -X ${fasta_t} ${fasta_t} > ${paf_raw}"
 
-${minimap_exec} -t ${nb_threads} -X ${fasta_q} ${fasta_q} > ${paf_raw}
+${minimap_exec} -t ${nb_threads} -X ${fasta_t} ${fasta_t} > ${paf_raw}
 
 fi
 

js/dgenies.run.js

@@ -243,9 +243,9 @@ dgenies.run.valid_form = function () {
     }
 
     //Check input query:
-    if ($("input#query").val().length === 0) {
-        $("label.file-query").addClass("error");
-        dgenies.run.add_error("Query fasta is required!");
+    if ($("input#target").val().length === 0) {
+        $("label.file-target").addClass("error");
+        dgenies.run.add_error("Target fasta is required!");
         has_errors = true;
     }
 
@@ -276,7 +276,7 @@ dgenies.run.reset_errors = function() {
 
 dgenies.run.start_uploads = function() {
     let query_type = parseInt($("select.query").val());
-    if (query_type === 0) {
+    if (query_type === 0 && $("input#query").val().length > 0) {
         $("button#button-query").hide();
         dgenies.run.show_loading("query");
     }

lib/job_manager.py

@@ -84,10 +84,8 @@ class JobManager:
 
     @db_session
     def __launch_local(self):
-        cmd = ["run_minimap2.sh", self.minimap2, self.threads,
-               self.target.get_path() if self.target is not None else "NONE", self.query.get_path(),
-               self.query.get_name(), self.target.get_name() if self.target is not None else "NONE", self.paf,
-               self.paf_raw, self.output_dir]
+        cmd = ["run_minimap2.sh", self.minimap2, self.threads, self.target.get_path(),
+               self.query.get_path() if self.query is not None else "NONE", self.paf, self.paf_raw]
         with open(self.logs, "w") as logs:
             p = subprocess.Popen(cmd, stdout=logs, stderr=logs)
         job = Job.get(id_job=self.id_job)
@@ -184,13 +182,13 @@ class JobManager:
                     job = Job.get(id_job=self.id_job)
                     job.status = "indexing"
                     db.commit()
-                    query_index = os.path.join(self.output_dir, "query.idx")
-                    Functions.index_file(self.query, query_index)
                     target_index = os.path.join(self.output_dir, "target.idx")
-                    if self.target is not None:
-                        Functions.index_file(self.target, target_index)
+                    Functions.index_file(self.target, target_index)
+                    query_index = os.path.join(self.output_dir, "query.idx")
+                    if self.query is not None:
+                        Functions.index_file(self.query, query_index)
                     else:
-                        shutil.copyfile(query_index, target_index)
+                        shutil.copyfile(target_index, query_index)
                     job = Job.get(id_job=self.id_job)
                     job.status = "success"
                     db.commit()
@@ -210,7 +208,7 @@ class JobManager:
         if len(j1) > 0:
             print("Old job found without result dir existing: delete it from BDD!")
             j1.delete()
-        if self.query is not None:
+        if self.target is not None:
             job = Job(id_job=self.id_job, email=self.email, batch_type=self.batch_system_type,
                       date_created=datetime.datetime.now())
             db.commit()

srv/main.py

@@ -91,8 +91,8 @@ def launch_analysis():
     if email == "":
         errors.append("Email not given")
         form_pass = False
-    if file_query == "":
-        errors.append("No query fasta selected")
+    if file_target == "":
+        errors.append("No target fasta selected")
         form_pass = False
 
     # Form pass
@@ -107,16 +107,16 @@ def launch_analysis():
         os.makedirs(folder_files)
 
         # Save files:
-        query_name = os.path.splitext(file_query.replace(".gz", ""))[0] if file_query_type == "local" else None
-        query_path = os.path.join(app.config["UPLOAD_FOLDER"], session["user_tmp_dir"], file_query) \
-            if file_query_type == "local" else file_query
-        query = Fasta(name=query_name, path=query_path, type_f=file_query_type)
-        target = None
-        if file_target != "":
-            target_name = os.path.splitext(file_target.replace(".gz", ""))[0] if file_target_type == "local" else None
-            target_path = os.path.join(app.config["UPLOAD_FOLDER"], session["user_tmp_dir"], file_target) \
-                if file_target_type == "local" else file_target
-            target = Fasta(name=target_name, path=target_path, type_f=file_target_type)
+        query = None
+        if file_query != "":
+            query_name = os.path.splitext(file_query.replace(".gz", ""))[0] if file_query_type == "local" else None
+            query_path = os.path.join(app.config["UPLOAD_FOLDER"], session["user_tmp_dir"], file_query) \
+                if file_query_type == "local" else file_query
+            query = Fasta(name=query_name, path=query_path, type_f=file_query_type)
+        target_name = os.path.splitext(file_target.replace(".gz", ""))[0] if file_target_type == "local" else None
+        target_path = os.path.join(app.config["UPLOAD_FOLDER"], session["user_tmp_dir"], file_target) \
+            if file_target_type == "local" else file_target
+        target = Fasta(name=target_name, path=target_path, type_f=file_target_type)
 
         # Launch job:
         job = JobManager(id_job, email, query, target, mailer)