snakemake expand config
时间: 2023-08-25 22:04:02 浏览: 41
Snakemake's `expand` function allows you to generate multiple output files or input files based on a template and a list of wildcards. It is particularly useful when you want to create dynamic rules or handle cases where the number of output files is not known in advance.
To use `expand`, you need to import it from the `snakemake` module. Here's an example of how you can use it:
```python
from snakemake import expand
# Define a wildcard pattern in your rule
wildcards = {"sample": ["A", "B", "C"], "replicate": [1, 2]}
# Define a template that includes the wildcards
template = "{sample}_{replicate}.txt"
# Use expand to generate a list of all possible combinations
files = expand(template, **wildcards)
# Now 'files' will contain a list of all possible combinations:
# ['A_1.txt', 'A_2.txt', 'B_1.txt', 'B_2.txt', 'C_1.txt', 'C_2.txt']
```
In this example, the `wildcards` dictionary contains two keys: "sample" and "replicate". Each key maps to a list of values that represent the possible values for that wildcard. The `template` variable is a string that includes placeholders for the wildcards. By calling `expand(template, **wildcards)`, Snakemake will generate all possible combinations by replacing the placeholders with the values from the wildcards.
You can then use the `files` list in your Snakemake rule to specify the input or output files.