d2 generation Snakefile

.gitignore

@@ -3,3 +3,4 @@ art/
 **/__pycache__/
 .pytest_cache/
 .idea/
+.snakemake/

Snakefile

+
+WORKDIR = "snake_tests"
+DATA = "data"
+
+rule all:
+    input:
+        f"{WORKDIR}/small_bar.tar.gz"
+
+
+rule compress_data:
+    input:
+        barcode_graph=f"{WORKDIR}/{{barcode_file}}.gexf",
+        d2_raw=f"{WORKDIR}/{{barcode_file}}_d2_raw.gexf",
+        simplified_d2=f"{WORKDIR}/{{barcode_file}}_d2_simplified.gexf"
+    output:
+        zip=f"{WORKDIR}/{{barcode_file}}.tar.gz"
+    shell:
+        f"mkdir {WORKDIR}/{{wildcards.barcode_file}};"
+        f"mv {WORKDIR}/*.gexf {WORKDIR}/{{wildcards.barcode_file}}/ ;"
+        f"tar czf {{output.zip}} {WORKDIR}/{{wildcards.barcode_file}}/ ;"
+        f"rm -rf {WORKDIR}/{{wildcards.barcode_file}}/ ;"
+
+
+rule d2_simplification:
+    input:
+        barcode_graph="{barcode_path}.gexf",
+        d2_raw="{barcode_path}_d2_raw.gexf"
+    output:
+        simplified_d2="{barcode_path}_d2_simplified.gexf"
+    shell:
+        "python3 deconvolution/d2_reduction.py -o {output.simplified_d2} {input.barcode_graph} {input.d2_raw}"
+
+
+rule d2_generation:
+    input:
+        barcode_graph=f"{WORKDIR}/{{file}}.gexf"
+    output:
+        d2_file=f"{WORKDIR}/{{file}}_d2_raw.gexf"
+    shell:
+        f"python3 deconvolution/to_d2_graph.py {{input.barcode_graph}} -o {WORKDIR}/{{wildcards.file}}_d2_raw"
+
+
+rule setup_workdir:
+    input:
+        barcode_graph=f"{DATA}/{{file}}.gexf"
+    output:
+        f"{WORKDIR}/{{file}}.gexf"
+    shell:
+        f"if [ ! -d {WORKDIR} ]; then mkdir {WORKDIR}; fi;"
+        f"cp {{input.barcode_graph}} {WORKDIR}"