update snakefile for evaluate d2 graphs

Snakefile_d2

@@ -13,7 +13,7 @@ INPUT = INPUT if isinstance(INPUT, list) else [INPUT]
 SAMPLE_NAME = [name[name.rfind('/')+1:name.rfind('.')] for name in INPUT]
 
 
-rule all:
+rule final_d2_files:
     input:
         expand(f"{WORKDIR}/{{name}}{final_output_suffix}", name=SAMPLE_NAME)
 
@@ -22,8 +22,6 @@ rule compress_data:
         barcode_graph=f"{WORKDIR}/{{barcode_file}}.gexf",
         d2_raw=f"{WORKDIR}/{{barcode_file}}_d2_raw_maxclq.gexf",
         simplified_d2=f"{WORKDIR}/{{barcode_file}}_d2_simplified_maxclq.gexf"
-        # d2_raw_louvain=f"{WORKDIR}/{{barcode_file}}_d2_raw_louvain.gexf",
-        # simplified_d2_louvain=f"{WORKDIR}/{{barcode_file}}_d2_simplified_louvain.gexf"
     output:
         zip=f"{WORKDIR}/{{barcode_file}}.tar.gz"
     shell:

Snakefile_d2_eval

+include: "Snakefile_data_simu"
+include: "Snakefile_d2"
+
+WORKDIR = "snake_experiments" if "workdir" not in config else config["workdir"]
+N = [5000, 10000]
+D = [10]
+M = [2, 3]
+DEV = [0, 1]
+
+rule eval_finalization:
+    input:
+         expand(f"{WORKDIR}/simu_0_bar_n{{n}}_d{{d}}_m{{m}}-dev{{dev}}_d2_simplified_maxclq_eval.txt", m=M, d=D, n=N, dev=DEV)
+
+rule eval:
+    input:
+        "{file}_d2_simplified_maxclq.gexf"
+    output:
+        "{file}_d2_simplified_maxclq_eval.txt"
+    shell:
+        "python3 deconvolution/main/evaluate.py -t d2 {input} > {output}"

Snakefile_data_simu

 
-OUTDIR="snake_exec" if "outdir" not in config else config["outdir"]
+WORKDIR="snake_exec" if "outdir" not in config else config["outdir"]
 N=[10000] if "n" not in config else config["n"] # Number of molecule to simulate
 D=[5] if "d" not in config else config["d"] # Average coverage of each molecule
 M=[2] if "m" not in config else config["m"] # Average number of molecule per barcode
 M_DEV=[0] if "m_dev" not in config else config["m_dev"] # Std deviation for merging number
 
+# snake_experiments/simu_0_bar_n500_d5_m2.gexf
 
 rule all:
     input:
-        expand(f"{OUTDIR}/simu_bar_n{{n}}_d{{d}}_m{{m}}-dev{{md}}.gexf", n=N, m=M, d=D, md=M_DEV)
+        expand(f"{WORKDIR}/simu_bar_n{{n}}_d{{d}}_m{{m}}-dev{{md}}.gexf", n=N, m=M, d=D, md=M_DEV)
 
-rule generate_barcodes:
+rule generate_barcodes_with_dev:
     input:
         "{path}/simu_mol_{params}.gexf"
     output:
-        "{path}/simu_bar_{params}_m{m}-dev{md}.gexf"
+        "{path}/simu{name}_bar_{params}_m{m}-dev{md}.gexf"
+    wildcard_constraints:
+        m="[0-9]+"
     shell:
         "python3 deconvolution/main/generate_fake_barcode_graph.py --merging_depth {wildcards.m} --deviation {wildcards.md} --input_graph {input} --output {output}"
 
+# snake_experiments/simu_0_bar_n500_d5_m2_d2_raw_maxclq.gexf
+rule generate_barcodes_without_dev:
+    input:
+        "{path}/simu_mol_{params}.gexf"
+    output:
+        "{path}/simu{name}_bar_{params}_m{m}.gexf"
+    wildcard_constraints:
+        m="[0-9]+"
+    shell:
+        "python3 deconvolution/main/generate_fake_barcode_graph.py --merging_depth {wildcards.m} --input_graph {input} --output {output}"
+
 rule generate_molecules:
     output:
         "{path}/simu_mol_n{n}_d{d}.gexf"