CODEWITHSUNDEEP
snakemake
Masih
Masih

Reputation: 980

InputFunctionException with KeyError

Suppose I have a code in python that generates a dictionary as the result. I need to write each element of dictionary in a separate folder which later will be used by other set of rules in snakemake. I have written the code as following but it does not work!

simulation_index_dict={1:'test1',2:'test2'}


def indexer(wildcards):
    return(simulation_index_dict[wildcards.simulation_index])

rule SimulateAll:
       input:
        expand("{simulation_index}/ProteinCodingGene/alfsim.drw",simulation_index=simulation_index_dict.keys())



rule simulate_phylogeny:
    output:
        ProteinCodingGeneParams=expand("{{simulation_index}}/ProteinCodingGene/alfsim.drw"),
        IntergenicRegionParams=expand("{{simulation_index}}/IntergenicRegions/dawg_IR.dawg"),
        RNAGeneParams=expand("{{simulation_index}}/IntergenicRegions/dawg_RG.dawg"),
        RepeatRegionParams=expand("{{simulation_index}}/IntergenicRegions/dawg_RR.dawg"),
    params:
        value= indexer,
    shell:
        """
        echo {params.value} > {output.ProteinCodingGeneParams}
        echo {params.value} > {output.IntergenicRegionParams}
        echo {params.value} > {output.RNAGeneParams}
        echo {params.value} > {output.RepeatRegionParams}
        """

The error it return is :

InputFunctionException in line 14 of /$/test.snake:
KeyError: '1'
Wildcards:
simulation_index=1

It seems that problems is with the params section of the rule because deleting it will eliminates the error but I can not figure out what is wrong with the params!

Upvotes: 2

Views: 3358

Answers (1)

bli
bli

Reputation: 8184

The solution: using strings as dictionary keys

One can guess from the error message (KeyError: '1') that some query in a dictionary went wrong on a key that is '1', which happens to be a string.

However, the dictionary used in the indexer "params" function has integers as keys.

Apparently, using strings instead of ints as keys to this simulation_index_dict dictionary solves the problem (see comments below the question).

The cause: loss of type information during workflow inference

The cause of the problem is likely that the integer nature (inherited from simulation_index_dict.keys()) of the value assigned to the simulation_index parameter of the expand in SimulateAll is "forgotten" in subsequent steps of the workflow inference.

Indeed, the expand results in a list of strings, which are then matched against the output of the other rules (which also consist in strings), to infer the values of the wildcards attributes (which are also strings). Therefore, when the indexer function is executed, wildcards.simulation_index is a string, and this causes a KeyError when looking it up in simulation_index_dict.

Upvotes: 1

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