rename d2 mains to lcpg mains

README.md

@@ -60,15 +60,17 @@ Config parameters:
 
 ### Data structures and algorithms
 
-* Create a d2 graph from barcode graph: use the snakemake "Snakefile_d2"  
+* Create a lcp graph from barcode graph: use the snakemake "Snakefile_lcpg"  
 The result will be generate as a compressed file in the workdir.  
 Config parameters:
 
   * input: the input barcode graph (gexf format preferred).
   * workdir: The working and output directory.
 
-* to_d2_graph.py: Mount a barcode graph into memory and create a d2 graph from it.
+* barcode_to_lcp_graph.py: Mount a barcode graph into memory and create a lcp graph from it.
 
-* d2_to_path.py: take a d2 graph as input and explore the nodes to extract a udg path.
+* lcpg_reduction.py: Perform a triplet transitive reduction on a lcp graph.
 
-* evaluate.py: take a d2 graph gexf file and and analyse it. Look for an approximation of the longest correct path to reconstruct a molecule graph. Take as input a d2 graph where the truth is known in the node names (the format used to create fake data).
+* lcpg_to_path.py: take a lcp graph as input and explore the nodes to extract a lcp path.
+
+* evaluate.py: take a lcp graph gexf file and and analyse it. Look for an approximation of the longest correct path to reconstruct a molecule graph. Take as input a lcp graph where the truth is known in the node names (the format used to create fake data). Can also evaluate a lcp path.

Snakefile_d2_eval

 include: "Snakefile_data_simu"
-include: "Snakefile_d2"
+include: "Snakefile_lcpg"
 include: "Snakefile_d2_path"
 
 WORKDIR = "snake_experiments" if "workdir" not in config else config["workdir"]
-N = [5000]
-D = [10]
+N = [500]
+D = [6]
 M = [2]
 DEV = [0]
 

Snakefile_d2_path

@@ -11,7 +11,7 @@ rule d2_path_generation:
     run:
         best = 0
         for _ in range(number_try):
-            shell("python3 deconvolution/main/d2_to_path.py {input.d2} > {output}_tmp.out")
+            shell("python3 deconvolution/main/lcpg_to_path.py {input.d2} > {output}_tmp.out")
             score = 0
             with open(f"{output}_tmp.out") as out:
                 score_line = out.readlines()[-2].strip()

Snakefile_d2 → Snakefile_lcpg

@@ -33,7 +33,7 @@ rule compress_data:
         "rm -rf {wildcards.barcode_file}/ ;"
         "cd - ;"
 
-rule d2_simplification:
+rule lcpg_simplification:
     input:
         d2_raw="{barcode_path}_d2_raw_{method}.gexf"
     output:
@@ -41,10 +41,10 @@ rule d2_simplification:
     wildcard_constraints:
         method="[A-Za-z0-9]+"
     shell:
-        "python3 deconvolution/main/d2_reduction.py -o {output.simplified_d2} {input.d2_raw}"
+        "python3 deconvolution/main/lcpg_reduction.py -o {output.simplified_d2} {input.d2_raw}"
 
 
-rule d2_generation:
+rule lcpg_generation:
     input:
         barcode_graph=f"{WORKDIR}/{{file}}.gexf"
     output:
@@ -53,7 +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}}.gexf")
+        shell(f"python3 deconvolution/main/barcode_to_lcp_graph.py {{input.barcode_graph}} --{{wildcards.method}} -t {{threads}} -o {WORKDIR}/{{wildcards.file}}_d2_raw_{{wildcards.method}}.gexf")
 
 
 rule setup_workdir: