Snakemake: Manually creating a wildcard from a string-CodePudding

Suppose I have two strings, a template and target string.

Template string: "param1~{wildcard1}/param2~{wildcard2}_param3~{wildcard3}"

Target string: "param1~1.1/param2~a_b_c_param3~345"

I would like to create a function that takes in a template string and target string as arguments. The function returns a wildcard object (or dictionary, or some data structure that can hold key-value pairs) where the key is the wildcard name (i.e wildcard1) and the value is the value of the wildcard in the target string (i.e 1.1)

Here's a little example:

def extract_wildcards(template, target):
    ... (implementation) ...
    return wildcards

Usage:

wildcards = extract_wildcards("param1~{wildcard1}/param2~{wildcard2}_param3~{wildcard3}",
                              "param1~1.1/param2~a_b_c_param3~345")
print(wildcards.wildcard1)
>"1.1"
print(wildcards.wildcard2)
>"a_b_c"
print(wildcards.wildcard3)
>"345"

Note that type casting is not necessary! All the values should strings. Wildcard names in the template will always be surrounded by {}. For the target string, you can assume that there is always only 1 way to extract wildcard values (no ambiguity in terms of what the each wildcard can be)

CodePudding user response：

This works for your example. The idea is to turn the snakemake string into a regex pattern and extract the matches. There might be some weirdness if the filename ends up producing unexpected regex patterns so keep that in mind.

import re

def extract_wildcards(template, target):
    names = re.findall("{[^{]*}", template)
    names = [name.strip("{}") for name in names]
    
    q = re.sub("{[^{]*}", "(.*)", template)
    matches = re.search(q, target)

    wildcards = dict()
    for i,name in enumerate(names):
        wildcards[name] = matches.group(i 1)
    return wildcards

example:

template="param1~{wildcard1}/param2~{wildcard2}_param3~{wildcard3}"
target="param1~1.1/param2~a_b_c_param3~345"
print(extract_wildcards(template, target))
  > {'wildcard1': '1.1', 'wildcard2': 'a_b_c', 'wildcard3': '345'}

I'm not sure what the goal of doing this is but it doesn't feel like a very "snakmake"-esqe solution. Have you considered trying an input function? https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=function#input-functions This type of function gets passed the wildcards automatically

CodePudding user response：

This is what snakemake uses internally:

template = "param1~{wildcard1}/param2~{wildcard2}_param3~{wildcard3}"
target = "param1~1.1/param2~a_b_c_param3~345"

# pip install parse
from parse import parse

wildcards = parse(template, target).named
print(wildcards)
# {'wildcard1': '1.1', 'wildcard2': 'a_b_c', 'wildcard3': '345'}

This should be bundled with snakemake (as an external dependency), in case it's not, one can install parse via pip:

pip install parse