feat: Allow paramspace to separate filename params with custom separa…

…tor (#1299)

* Allow paramspace to separate filename params with custom separator

* Add test for 'filename_sep'

* Add missing files

* Use filename separator in tests which hopefully works better on windows

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

snakemake/utils.py

@@ -608,7 +608,7 @@ class Paramspace:
     By default, a directory structure with on folder level per parameter is created
     (e.g. column1~{column1}/column2~{column2}/***).
 
-    The exact behavior can be tweaked with two parameters:
+    The exact behavior can be tweaked with three parameters:
 
       - ``filename_params`` takes a list of column names of the passed dataframe.
         These names are used to build the filename (separated by '_') in the order
@@ -622,16 +622,26 @@ class Paramspace:
         If ``filename_params="*"``, all columns of the dataframe are encoded into
         the filename instead of parent directories.
 
-      - ``param_sep`` takes a string that is used to join the column name and
+      - ``param_sep`` takes a string which is used to join the column name and
         column value in the generated paths (Default: '~'). Example:
 
         | ``Paramspace(df, param_sep=":")`` ->
         | column1:{value1}/column2:{value2}/column3:{value3}/column4:{value4}
+
+      - ``filename_sep`` takes a string which is used to join the parameter
+        entries listed in ``filename_params`` in the generated paths
+        (Default: '_'). Example:
+
+        | ``Paramspace(df, filename_params="*", filename_sep="-")`` ->
+        | column1~{value1}-column2~{value2}-column3~{value3}-column4~{value4}
     """
 
-    def __init__(self, dataframe, filename_params=None, param_sep="~"):
+    def __init__(
+        self, dataframe, filename_params=None, param_sep="~", filename_sep="_"
+    ):
         self.dataframe = dataframe
         self.param_sep = param_sep
+        self.filename_sep = filename_sep
         if filename_params is None or not filename_params:
             # create a pattern of the form {}/{}/{} with one entry for each
             # column in the dataframe
@@ -653,7 +663,7 @@ def __init__(self, dataframe, filename_params=None, param_sep="~"):
             self.pattern = "/".join(
                 [r"{}"] * (len(self.dataframe.columns) - len(filename_params) + 1)
             )
-            self.pattern = "_".join(
+            self.pattern = self.filename_sep.join(
                 [self.pattern] + [r"{}"] * (len(filename_params) - 1)
             )
             self.ordered_columns = [

tests/test_paramspace/Snakefile

@@ -2,34 +2,41 @@ from snakemake.utils import Paramspace
 import pandas as pd
 
 
-# shold result in alpha~{alpha}/beta~{beta}/gamma~{gamma}
+# should result in alpha~{alpha}/beta~{beta}/gamma~{gamma}
 paramspace_default = Paramspace(pd.read_csv("params.tsv", sep="\t"))
 
-# shold result in alpha~{alpha}/beta~{beta}/gamma~{gamma}
+# should result in alpha~{alpha}/beta~{beta}/gamma~{gamma}
 paramspace_empty = Paramspace(pd.read_csv("params.tsv", sep="\t"), filename_params=[])
 
-# shold result in alpha~{alpha}/gamma~{gamma}/beta~{beta}
+# should result in alpha~{alpha}/gamma~{gamma}/beta~{beta}
 paramspace_one = Paramspace(pd.read_csv("params.tsv", sep="\t"), filename_params=["beta"])
 
-# shold result in alpha~{alpha}/beta~{beta}_gamma~{gamma}
+# should result in alpha~{alpha}/beta~{beta}_gamma~{gamma}
 paramspace_two = Paramspace(pd.read_csv("params.tsv", sep="\t"), filename_params=["beta", "gamma"])
 
-# shold result in alpha~{alpha}_beta~{beta}_gamma~{gamma}
+# should result in alpha~{alpha}_beta~{beta}_gamma~{gamma}
 paramspace_full = Paramspace(pd.read_csv("params.tsv", sep="\t"), filename_params=["alpha", "beta", "gamma"])
 
-# shold result in beta~{beta}_gamma~{gamma}_alpha~{alpha}
+# should result in beta~{beta}_gamma~{gamma}_alpha~{alpha}
 paramspace_full_reorder = Paramspace(pd.read_csv("params.tsv", sep="\t"), filename_params=["beta", "gamma", "alpha"])
 
-# shold result in alpha:{alpha}/beta:{beta}/gamma:{gamma}
+# should result in alpha:{alpha}/beta:{beta}/gamma:{gamma}
 paramspace_sep = Paramspace(pd.read_csv("params.tsv", sep="\t"), param_sep="_is_")
 
-# shold result in beta={beta}_gamma={gamma}_alpha={alpha}
+# should result in beta={beta}_gamma={gamma}_alpha={alpha}
 paramspace_sep_and_pattern = Paramspace(
     pd.read_csv("params.tsv", sep="\t"),
     filename_params=["beta", "gamma", "alpha"],
     param_sep="=",
 )
 
+# should result in alpha~{alpha}::beta~{beta}::gamma~{gamma}
+paramspace_filenamesep = Paramspace(
+    pd.read_csv("params.tsv", sep="\t"),
+    filename_params="*",
+    filename_sep="__",
+)
+
 
 rule all:
     input:
@@ -41,6 +48,7 @@ rule all:
         expand("results/full_reorder/plots/{params}.pdf", params=paramspace_full_reorder.instance_patterns),
         expand("results/sep/plots/{params}.pdf", params=paramspace_sep.instance_patterns),
         expand("results/sep_and_pattern/plots/{params}.pdf", params=paramspace_sep_and_pattern.instance_patterns),
+        expand("results/filenamesep/plots/{params}.pdf", params=paramspace_filenamesep.instance_patterns),
 
 
 rule simulate_default:
@@ -185,3 +193,21 @@ rule plot_sep_and_pattern:
         f"results/sep_and_pattern/plots/{paramspace_sep_and_pattern.wildcard_pattern}.pdf"
     shell:
         "touch {output}"
+
+
+rule simulate_filenamesep:
+    output:
+        f"results/filenamesep/simulations/{paramspace_filenamesep.wildcard_pattern}.tsv"
+    params:
+        simulation=paramspace_filenamesep.instance
+    script:
+        "scripts/simulate.py"
+
+
+rule plot_filenamesep:
+    input:
+        f"results/filenamesep/simulations/{paramspace_filenamesep.wildcard_pattern}.tsv"
+    output:
+        f"results/filenamesep/plots/{paramspace_filenamesep.wildcard_pattern}.pdf"
+    shell:
+        "touch {output}"

tests/test_paramspace/expected-results/results/filenamesep/simulations/alpha~1.0__beta~0.1__gamma~0.99.tsv

@@ -0,0 +1 @@
+{'alpha': 1.0, 'beta': 0.1, 'gamma': 0.99}

tests/test_paramspace/expected-results/results/filenamesep/simulations/alpha~2.0__beta~0.0__gamma~3.9.tsv

@@ -0,0 +1 @@
+{'alpha': 2.0, 'beta': 0.0, 'gamma': 3.9}