snakemake use wildcard input/output in python function

Question

I Have a simple python function that take an input and create an output

def enlarge_overlapping_region(input,output):
    fi=open(input,"r")
    fo=open(output,"w")
    df = pd.read_table(fi, delimiter='\t',header=None,names=["chr","start","end","point","score","strand","cdna_count","lib_count","region_type","region_id"])
    df1 = (df.groupby('region_id', as_index=False)
         .agg({'chr':'first', 'start':'min', 'end':'max','region_type':'first'})
         [['chr','start','end','region_type','region_id']])
    df1 = df1[df1.region_id != "."]
    df1.to_csv(fo,index=False, sep='\t')

    return(df1)

I call this function in a rule snakemake. But I cannot access to the file I don't know why.

I tried something like that :

rule get_enlarged_dhs:
    input:
        "data/annotated_clones/{cdna}_paste_{lib}.annotated.bed"
    output:
        "data/enlarged_coordinates/{cdna}/{cdna}_paste_{lib}.enlarged_dhs.bed"
    run:
        lambda wildcards: enlarge_overlapping_region(f"{wildcards.input}",f"{wildcards.output}")

I got this error :

Missing files after 5 seconds:
data/enlarged_coordinates/pPGK_rep1/pPGK_rep1_paste_pPGK_input.enlarged_dhs.bed
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wa
it.

If I put directly the python code into the rule like thath :

rule get_enlarged_dhs:
    input:
        "data/annotated_clones/{cdna}_paste_{lib}.annotated.bed"
    output:
        "data/enlarged_coordinates/{cdna}/{cdna}_paste_{lib}.enlarged_dhs.bed"
    run:
        fi=open(input,"r")
        fo=open(output,"w")
        df = pd.read_table(fi, delimiter='\t',header=None,names=["chr","start","end","point","score","strand","cdna_count","lib_count","region_type","region_id"])
        df1 = (df.groupby('region_id', as_index=False)
             .agg({'chr':'first', 'start':'min', 'end':'max','region_type':'first'})
             [['chr','start','end','region_type','region_id']])
        df1 = df1[df1.region_id != "."]
        df1.to_csv(fo,index=False, sep='\t')

I got this error :

expected str, bytes or os.PathLike object, not InputFiles

Answer 1

It's simpler than you think, probably:

lambda wildcards: enlarge_overlapping_region(f"{wildcards.input}",f"{wildcards.output}")

Should be:

enlarge_overlapping_region(input[0], output[0])

Similarly, to fix the second solution you tried change:

fi=open(input,"r")
fo=open(output,"w")

to

fi=open(input[0],"r")
fo=open(output[0],"w")

---

In my opinion, it's less error-prone to assign a name to input and output files and use that name in the run or shell directives. E.g.

rule get_enlarged_dhs:
    input:
        bed= "...",
    output:
        bed= "...",
    run:
        enlarge_overlapping_region(input.bed, output.bed)