How to get a rule that would work the same on a directory and its sub-directories

user_2082836 0
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I am trying to make a rule that would work the same on a directory and any of its sub sub-directory (to avoid having to repeat the rule several times). I would like to have access to the name of the subdirectory if there is one.

My approach was to make the sub-directory optional. Given that wildcards can be made to accept an empty string by explicitly giving the ".*" pattern, I therefore tried the following rule:

rule test_optional_sub_dir:
    input:
        "{adir}/{bdir}/a.txt"
    output:
        "{adir}/{bdir,.*}/b.txt"
    shell:
        "cp {input} {output}"

I was hoping that this rule would match both A/b.txt and A/B/b.txt.

However, A/b.txt doesn't match the rule. (Neither does A//b.txt which would be the litteral omission of bdir, I guess the double / gets removed before the matching happens).

The following rule works with both A/b.txt and A/B/b.txt:

rule test_optional_sub_dir2:
    input:
        "{path}/a.txt"
    output:
        "{path,.*}/b.txt"
    shell:
        "cp {input} {output}"

but the problem in this case is that I don't have easy access to the name of the directories in path. I could use the function pathlib.Path to break {path} up but this seems to get overly complicated.

Is there a better way to accomplish what I am trying to do?

Thanks a lot for your help.

snakemake
2 Answers

With some further fiddling, I found something that is close to what I want: Let's say I want at least one directory and no more than 2 optional ones below it. The following works. The only downside is that opt_dir1 and opt_dir2 contain the trailing slash rather than just the name of the directory.

rule test_optional_sub_dir3:
    input:
        "{mand_dir}/{opt_dir1}{opt_dir2}a.txt"
    output:
        "{mand_dir}/{opt_dir1}{opt_dir2}b.txt"
    wildcard_constraints:
        mand_dir="[^/]+",
        opt_dir1="([^/]+/)?",
        opt_dir2="([^/]+/)?"
    shell:
        "cp {input} {output}"

Still interested in better approaches if anyone has one.

user_20828360

How exactly you want to use the sub-directory in your rule might determine the best way to do this. Maybe something like:

def get_subdir(path):
    dirs = path.split('/')
    if len(dirs) > 1:
        return dirs[1]
    else:
        return ''

rule myrule:
    input:
        "{dirpath}/a.txt"
    output:
        "{dirpath}/b.txt"
    params:
        subdir = lambda wildcards: get_subdir(wildcards.dirpath)
    shell:
        #use {params.subdir}

Of course, if your rule uses "run" or "script" instead of "shell" you don't even need that function and the subdir param, and can just figure out the subdir from the wildcard that gets passed into the script.

user_2512760
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