Merge branch 'dev' into 'main'

fix bug display proteins when mutiple nt contigs as input

See merge request !16

backend/analysis/models.py

@@ -261,11 +261,10 @@ class Analysis(Invocation):
         queryset = Protein.objects.filter(analysis=self)
         if self.status == DONE and queryset.count() == 0:
             file_path = self.load_dataset("proteins", "proteins")
-            proteins = self.read_fasta_file(file_path)
+            proteins = self.read_fasta_file(file_path, isFromNt=True)
             if len(proteins) <= 1:
                 file_path = self.load_dataset("sequences", "proteins")
                 proteins = self.read_fasta_file(file_path)
-            # print(proteins)
             json_prots = [ProteinEntry(**prot).dict() for prot in proteins]
 
             prots = Protein(analysis=self, proteins=json_prots)
@@ -283,24 +282,47 @@ class Analysis(Invocation):
                 self.stderr = job.wrapped["tool_stderr"]
                 self.save()
 
-    def read_fasta_file(self, file_path):
+    def read_fasta_file(self, file_path, isFromNt=False):
+
+        # if is from Nt, need to sum prot length.
+        # In order to get proteins that belongs to same contig
+        # just remove (_\d+) to the id
+
         sequences = []
         if file_path is not None:
             with open(file_path) as handle:
-
+                current_contig = None
+                offset = 0
+                last_prot_end = 0
                 for record in SeqIO.parse(handle, "fasta"):
+
                     prot = {"id": record.id, "length": len(record), "strand": None}
+
+                    if isFromNt:
+                        contig = "-".join(prot["id"].split("_")[0:-1])
+                        if current_contig is None or contig != current_contig:
+                            current_contig = contig
+                            if current_contig is not None:
+                                offset = offset + last_prot_end
+                                print(offset)
+
                     description_list = record.description.split(" # ")
                     if len(description_list) == 5:
                         start = description_list[1]
                         end = description_list[2]
                         strand = description_list[3]
+
                         if strand == "1" or strand == "-1":
                             prot["strand"] = int(strand)
-                            prot["start"] = int(start)
-                            prot["end"] = int(end)
                         else:
                             strand = None
+                        if isFromNt:
+                            prot["start"] = offset + int(start)
+                            prot["end"] = offset + int(end)
+                            last_prot_end = prot["end"]
+                        else:
+                            prot["start"] = int(start)
+                            prot["end"] = int(end)
                     sequences.append(prot)
         return sequences