modification of snakefiles according to the refactored pieces

Snakefile_d2

@@ -35,14 +35,13 @@ rule compress_data:
 
 rule d2_simplification:
     input:
-        barcode_graph="{barcode_path}.gexf",
         d2_raw="{barcode_path}_d2_raw_{method}.gexf"
     output:
         simplified_d2="{barcode_path}_d2_simplified_{method}.gexf"
     wildcard_constraints:
         method="[A-Za-z0-9]+"
     shell:
-        "python3 deconvolution/main/d2_reduction.py -o {output.simplified_d2} {input.barcode_graph} {input.d2_raw}"
+        "python3 deconvolution/main/d2_reduction.py -o {output.simplified_d2} {input.d2_raw}"
 
 
 rule d2_generation:
@@ -54,7 +53,7 @@ rule d2_generation:
     wildcard_constraints:
         method="[A-Za-z0-9]+"
     run:
-        shell(f"python3 deconvolution/main/to_d2_graph.py {{input.barcode_graph}} --{{wildcards.method}} -t {{threads}} -o {WORKDIR}/{{wildcards.file}}_d2_raw_{{wildcards.method}}")
+        shell(f"python3 deconvolution/main/to_d2_graph.py {{input.barcode_graph}} --{{wildcards.method}} -t {{threads}} -o {WORKDIR}/{{wildcards.file}}_d2_raw_{{wildcards.method}}.gexf")
 
 
 rule setup_workdir:

Snakefile_d2_eval

@@ -3,10 +3,10 @@ include: "Snakefile_d2"
 include: "Snakefile_d2_path"
 
 WORKDIR = "snake_experiments" if "workdir" not in config else config["workdir"]
-N = [5000, 10000]
-D = [10]
-M = [2, 3]
-DEV = [0, 1]
+N = [500]
+D = [6]
+M = [2]
+DEV = [0]
 
 rule generate_compare:
     input:

Snakefile_d2_path

@@ -5,14 +5,13 @@ threshold = 0.9
 
 rule d2_path_generation:
     input:
-        barcode="{path}.gexf",
         d2="{path}_d2_{type}_{method}.gexf"
     output:
         "{path}_d2_{type}_{method}_path.gexf"
     run:
         best = 0
         for _ in range(number_try):
-            shell("python3 deconvolution/main/d2_to_path.py {input.barcode} {input.d2} > {output}_tmp.out")
+            shell("python3 deconvolution/main/d2_to_path.py {input.d2} > {output}_tmp.out")
             score = 0
             with open(f"{output}_tmp.out") as out:
                 score_line = out.readlines()[-2].strip()

deconvolution/main/to_d2_graph.py

@@ -10,7 +10,7 @@ from deconvolution.d2graph import d2_graph as d2
 def parse_arguments():
     parser = argparse.ArgumentParser(description='Transform a barcode graph into a lcp graph. The program dig for a set of lcps and then merge them into a lcp graph.')
     parser.add_argument('barcode_graph', help='The barcode graph file. Must be a gefx formated file.')
-    parser.add_argument('--output_prefix', '-o', default="",  help="Output file prefix.")
+    parser.add_argument('--outfile', '-o', default="",  help="Output file name for lcp graph.")
     parser.add_argument('--threads',       '-t', default=8, type=int, help='Number of thread to use for dgraph computation')
     parser.add_argument('--debug',         '-d', action='store_true', help="Debug")
     parser.add_argument('--verbose',         '-v', action='store_true', help="Verbose")
@@ -20,8 +20,8 @@ def parse_arguments():
 
     args = parser.parse_args()
 
-    if args.output_prefix == "":
-        args.output_prefix = ".".join(args.barcode_graph.split(".")[:-1]) + "_lcpg"
+    if args.outfile == "":
+        args.outfile = ".".join(args.barcode_graph.split(".")[:-1]) + "_lcpg.gexf"
 
     return args
 
@@ -43,7 +43,7 @@ def main():
     debug_path = "/dev/null"
     if args.debug:
         debug = True
-        debug_path = f"{args.output_prefix}_debug"
+        debug_path = ".".join(args.barcode_graph.split(".")[:-1]) + "_debug"
         import os, shutil
         if os.path.isdir(debug_path):
             shutil.rmtree(debug_path)
@@ -58,7 +58,7 @@ def main():
         verbose=args.verbose
     )
 
-    nx.write_gexf(d2g, f"{args.output_prefix}.gexf")
+    nx.write_gexf(d2g, args.outfile)
 
 
 if __name__ == "__main__":