Deepsignal1

rule extract_feature:
    input:
        fast5="data/{sample}",
        ref="data/ecoli_k12_mg1655.fasta"
    output:
        "deepsignal_results/{sample}_deepsignal-feature.tsv"
    shell:
        "tombo resquiggle --dna {input.fast5} {input.ref} --processes 10 --overwrite && deepsignal extract --fast5_dir {input.fast5} --reference_path {input.ref} --is_dna true --write_path {output} --nproc 10"

rule call_modification:
    input:
        "deepsignal_results/{sample}_deepsignal-feature.tsv",
    output:
        "deepsignal_results/{sample}_deepsignal-prob.tsv"
    shell:
        "deepsignal call_mods --input_path {input} --is_gpu no --nproc 10 --model_path data/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt --result_file {output}"

rule calculate_frequency:
    input:
        "deepsignal_results/{sample}_deepsignal-prob.tsv"
    output:
        "deepsignal_results/{sample}_deepsignal-freq-perCG-raw.tsv"
    shell:
        "python script_in_snakemake/call_modification_frequency.py --input_path {input} --result_file {output} --prob_cf 0"