add option to choose the path search mode

knot/AAG.rules

@@ -10,7 +10,7 @@ rule build_AGG:
         "{prefix}_AAG.csv"
 
     shell:
-        "python -m knot.path_search {input.search} {output} {input.ovl_graph} {input.read2asm} {input.asm_graph} {input.tig2tig}"
+        "python -m knot.path_search {input.search} {output} {input.ovl_graph} {input.read2asm} {input.asm_graph} {input.tig2tig} --search-mode " + config["search_mode"]
 
 rule filter_contigs:
     input:

knot/__main__.py

@@ -35,6 +35,8 @@ def main(args = None):
    
     parser.add_argument("-o", "--output", required=True,
                         help="output prefix")
+    parser.add_argument("--search-mode", choices=["base", "node"], default="base",
+                        help="what path search optimize, number of base or number of node")
     parser.add_argument("--contig-min-length", default=100000, type=int,
                         help="contig with size lower this parameter are ignored")
     parser.add_argument("--read-type", choices=["pb", "ont"], default="pb",
@@ -50,7 +52,7 @@ def main(args = None):
         parser.print_help()
         snakemake_help()
         return 1
-
+    
     ## if contig graph isn't set generate empty file
     if args["contigs_graph"] is None:
         args["contigs_graph"] = tempfile.NamedTemporaryFile(delete=False).name
@@ -65,6 +67,7 @@ def main(args = None):
         "contigs_graph="+args["contigs_graph"],
         "read_type="+args["read_type"],
         "min_contig_length="+str(args["contig_min_length"]),
+        "search_mode="+args["search_mode"],
         "package_path="+package_path
     ]
 

knot/path_search/__main__.py

@@ -37,6 +37,8 @@ def main(args=None):
     parser.add_argument("read2asm", type=argparse.FileType('r'))
     parser.add_argument("asm_graph", type=argparse.FileType('r'))
     parser.add_argument("tig2tig", type=argparse.FileType('r'))
+    parser.add_argument("--search-mode", choices=["base", "node"], default="base",
+                        help="what path search optimize, number of base or number of node")
 
     args = vars(parser.parse_args(args))
 
@@ -47,7 +49,6 @@ def main(args=None):
     # get info about contig
     valid_read = extremity_search.get_valid_read(args["ovl_graph"])
     tig2reads = {tig[0]: {v[2] for v in val} for tig, val in extremity_search.get_tig2posread(args["read2asm"], valid_read).items()}
-   
 
     # build list of search
     tig_ext = list()
@@ -72,7 +73,7 @@ def main(args=None):
             print(ext1[0], node1, ext2[0], node2, 0, 0, "not_search", "not_search", sep=",", file=args["result"])
             continue
 
-        (path, weight) = paths.get_path(sg, node1, node2)
+        (path, weight) = paths.get_path(sg, node1, node2, args["search_mode"])
         if path:
             nbread_contig = paths.format_node_contig_counter(
                 paths.path_through_contig(tig2reads, path),

knot/path_search/paths.py

@@ -5,10 +5,13 @@ from collections import Counter
 # pip import
 import networkx as nx
 
-def get_path(graph, n1, n2):
+def get_path(graph, n1, n2, mode="base"):
 
     try:
-        path = nx.shortest_path(graph, n1, n2, weight="weight")
+        if mode == "base":
+            path = nx.shortest_path(graph, n1, n2, weight="weight")
+        else:
+            path = nx.shortest_path(graph, n1, n2)
     except nx.exception.NetworkXError as e:
         logging.debug("Networkx exception"+str(e))
         path = []
@@ -18,8 +21,8 @@ def get_path(graph, n1, n2):
     except nx.exception.NodeNotFound as e:
         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:])]) 
+
+    return path, sum([graph.edges[x, y]["weight"] for x, y in zip(path, path[1:])])
 
 def path_through_contig(tig2reads, path):
     tig2nb_read = Counter()