Display CIGAR ins / del

ediacara/Comparator.py

@@ -63,6 +63,10 @@ def compute_feature_color(self, feature):
         ediacara_qualifier = "ediacara"
         if feature.qualifiers[ediacara_qualifier] == "assembly":
             return "#d3d3d3"
+        elif feature.qualifiers[ediacara_qualifier] == "deletion":
+            return "#f5685e"
+        elif feature.qualifiers[ediacara_qualifier] == "insertion":
+            return "#2a9d8f"
         else:
             return "#7245dc"  # default dna_features_viewer colour
 
@@ -384,6 +388,7 @@ def interpret_asm(self):
             self.wrong_length = False
 
         part_type = "assembly"  # all entries should be the assembly
+        # This section adds both a generic alignment feature, and one for each ins/del:
         for index, row in self.aln.iterrows():
 
             location = SeqFeature.FeatureLocation(
@@ -395,13 +400,51 @@ def interpret_asm(self):
                 id=row["query_name"],
                 qualifiers={"label": row["query_name"], "ediacara": part_type},
             )
-
             self.asm.features.append(feature)
+
+            cigar = row["CIGAR"].replace("cg:Z:", "")  # paf custom tag label
+            matches = re.findall(r"(\d+)([A-Z]{1})", cigar)
+            current_position = row["target_start"]  # in the ref
+            for length, change in matches:
+                if change == "M":
+                    current_position += int(length)
+                elif change == "D":
+                    new_position = current_position + int(length)
+                    feat_loc = SeqFeature.FeatureLocation(
+                        current_position, new_position
+                    )
+                    feat_id = "del" + length
+                    feature = SeqFeature.SeqFeature(
+                        location=feat_loc,
+                        type="misc_feature",
+                        id=feat_id,
+                        qualifiers={"label": feat_id, "ediacara": "deletion"},
+                    )
+                    current_position = new_position  # step forward after annotation
+                    self.asm.features.append(feature)
+
+                elif change == "I":
+                    # do not change position, insert is in query (asm)
+                    feat_loc = SeqFeature.FeatureLocation(
+                        current_position, current_position
+                    )
+                    feat_id = "ins" + length
+                    feature = SeqFeature.SeqFeature(
+                        location=feat_loc,
+                        type="misc_feature",
+                        id=feat_id,
+                        qualifiers={"label": feat_id, "ediacara": "insertion"},
+                    )
+                    self.asm.features.append(feature)
+                else:
+                    raise ValueError("Incorrect symbol in CIGAR")
+
+        # This should come after all feature additions:
         self.asm_figure = self.plot_aln()
 
         self.cigar_str = ""
         self.cigar_dict = {"M": [], "D": [], "I": []}  # see cigar definition
-        for entry in self.aln["CIGAR"]:  # conncatenate any entries
+        for entry in self.aln["CIGAR"]:  # concatenate any entries
             self.cigar_str += entry.replace("cg:Z:", "")  # paf custom tag label
         matches = re.findall(r"(\d+)([A-Z]{1})", self.cigar_str)
         for length, change in matches:

ediacara/reports.py

@@ -119,7 +119,7 @@ def tr_modifier(tr):
             comparatorgroup.fastq_plot, fmt="svg", size=[8, 3]
         )
         comparatorgroup.asm_figure_data = pdf_tools.figure_data(
-            comparatorgroup.asm_figure, fmt="svg", size=[8, 1]
+            comparatorgroup.asm_figure, fmt="svg", size=[8, 2]
         )
 
         comparatorgroup.aln_table = dataframe_to_html(