Correct biais in path weight computation

demo/Readme.md

@@ -24,5 +24,5 @@ knot -r reads_raw.fasta -c assembly_contig.fasta -g assembly_graph.gfa -o raw
 On corrected reads:
 
 ```
-knot -C reads_raw.fasta -c assembly_contig.fasta -g assembly_graph.gfa -o corrected
+knot -C reads_corrected.fasta -c assembly_contig.fasta -g assembly_graph.gfa -o corrected
 ```

knot/extremity_search/__init__.py

@@ -28,7 +28,7 @@ def get_tig2posread(read2tig, valid_read):
         if valid_read and row[0] not in valid_read:
             continue
         if int(row[3]) - int(row[2]) > 0.7 * int(row[1]):
-            result[(row[5], int(row[6]))].append((int(row[7]), int(row[8]), row[0], row[4]))
+            result[(row[5], int(row[6]))].append((int(row[7]), int(row[8]), row[0], int(row[2]), int(row[1]) - int(row[3]), row[4]))
 
     return result
 

knot/extremity_search/__main__.py

@@ -24,21 +24,43 @@ def main(args=None):
 
     valid_read = get_valid_read(args["read2read"]) # read name
     
-    tig2posread = get_tig2posread(args["read2tig"], valid_read) # tig -> (begin, end, name)
+    # (tig, tig_len) -> (tig_begin, tig_end, name, read_begin, read_dist_to_end, read_ori)
+    tig2posread = get_tig2posread(args["read2tig"], valid_read) 
     for k in tig2posread:
         tig2posread[k].sort()
 
-    print("tig","read","strand_to_tig", sep=",", file=args["output"])
+    print("tig","read","strand_to_tig","dist2ext", sep=",", file=args["output"])
 
     for tig in tig2posread.keys():
         ext = tig[0]+"_begin"
-        print(ext, tig2posread[tig][1][2], tig2posread[tig][1][3], 
-              sep=",", file=args["output"])
-        
+        print(tig, tig2posread[tig][1])
+        if tig2posread[tig][1][5] == "+":
+            print(ext,
+                  tig2posread[tig][1][2],
+                  tig2posread[tig][1][5],
+                  (tig2posread[tig][1][0] - tig2posread[tig][1][3]) * -1,
+                  sep=",", file=args["output"])
+        else:
+            print(ext,
+                  tig2posread[tig][1][2],
+                  tig2posread[tig][1][5],
+                  (tig2posread[tig][1][0] - tig2posread[tig][1][4]) * -1,
+                  sep=",", file=args["output"])
+            
         ext = tig[0]+"_end"
         tig2posread[tig].sort(key=lambda x: x[1])
-        print(ext, tig2posread[tig][-2][2], tig2posread[tig][-2][3],
-              sep=",", file=args["output"])
+        if tig2posread[tig][-2][5] == "+":
+            print(ext,
+                  tig2posread[tig][-2][2],
+                  tig2posread[tig][-2][5],
+                  ((tig[1] - tig2posread[tig][-2][1]) - tig2posread[tig][-2][4]) * -1,
+                  sep=",", file=args["output"])
+        else:
+            print(ext,
+                  tig2posread[tig][-2][2],
+                  tig2posread[tig][-2][5],
+                  ((tig[1] - tig2posread[tig][-2][1]) - tig2posread[tig][-2][3]) * -1,
+                  sep=",", file=args["output"])
 
 if __name__ == '__main__':
     main(sys.argv[1:])

knot/path_search/__main__.py

@@ -74,6 +74,10 @@ def main(args=None):
             continue
 
         (path, weight) = paths.get_path(sg, node1, node2, args["search_mode"])
+        if len(path) <= 2:
+            weight = 0
+        else:
+            weight -= int(ext1[3]) - int(ext2[3])
         if path:
             nbread_contig = paths.format_node_contig_counter(
                 paths.path_through_contig(tig2reads, path),

knot/path_search/gfa2sg.py

@@ -62,7 +62,9 @@ def __add_dovetails(d, G, is_contain):
                qual=qual_val,
                len=d.alignment.length_on_query(),
                overhang_len=d.to_segment.length - d.alignment.length_on_query(),
-               weight=int(d.to.LN-d.alignment.length_on_query()))
+               weight=int(d.to_segment.length-d.alignment.length_on_query()),
+               to_length = d.to_segment.length
+    )
 
 class isContain:
     

knot/path_search/paths.py

@@ -22,7 +22,14 @@ def get_path(graph, n1, n2, mode="base"):
         logging.debug("Node not found exception "+str(e))
         path = []
 
-    return path, sum([graph.edges[x, y]["weight"] for x, y in zip(path, path[1:])])
+    if not path:
+        return path, 0
+    
+    if len(path) == 2:
+        edge = graph.edges[path[0], path[1]]
+        return path, 0
+    
+    return path, sum([graph.edges[x, y]["weight"] for x, y in zip(path, path[1:])]) - graph.edges[path[-2], path[-1]]["to_length"]
 
 def path_through_contig(tig2reads, path):
     tig2nb_read = Counter()