Snakefile

rule all:
   input:
        "output/tRNA_scan_result.txt",
        "output/G_intestinalis.tRNA",
        "output/G_intestinalis.stats",
        "output/tRNAscan/G_intestinalis.tRNA",
        expand("output/tRNAscan/{sp}.tRNA", sp=["G_muris", "G_intestinalis"]),
        expand("output/blastn/G_intestinalis/{sp}.blastn", sp=["G_muris", "S_salmonicida"]),
        #expand("output/plot/tRNAscan/{sp}.svg", sp=["G_muris", "S_salmonicida", "G_intestinalis"])

rule tRNAscan:
   input: "resource/Genome/G_intestinalis.fasta"
   output:"output/tRNA_scan_result.txt"
   conda:
         "env/env.yaml"
   shell: """tRNAscan-SE {input} -o {output}"""
rule tRNAscan_stats:
   input:
        genome= "resource/Genome/G_intestinalis.fasta"
   output:
   	    tRNA = "output/G_intestinalis.tRNA",
   	    stats = "output/G_intestinalis.stats"
   params:
        threads= 2
   conda:
           "env/env.yaml"
   script:
           "scripts/tRNAscan_stats.py"
#rule tRNAscan_stats_wildcard:
#    input:
#            genome="resource/Genome/{Genome}.fasta"
#    output:
#            tRNA = "output/tRNAscan/{Genome}.tRNA",
#            stats = "output/tRNAscan/{Genome}.stats"
#    params:
#        threads=2
#    conda:
#        "env/env.yaml"
#    script:
#        "scripts/tRNAscan_stats.py"

rule makeblastdb:
    input:
        "resource/{type}/db/{db}.fasta"
    output:
        "output/{type}/db/{db}.ndb",
        "output/{type}/db/{db}.nhr",
        "output/{type}/db/{db}.nin",
        "output/{type}/db/{db}.not",
        "output/{type}/db/{db}.nsq",
        "output/{type}/db/{db}.ntf",
        "output/{type}/db/{db}.nto"
    params:
        outname="output/{type}/db/{db}"
    conda:
        "env/env.yaml"
    shell:
        'makeblastdb -dbtype nucl -in {input} -out {params.outname}'

rule blastn:
    input:
        query="resource/{type}/query/{query}.fasta",
        db="output/{type}/db/{db}.ndb"
    output:
        'output/{type}/{db}/{query}.blastn'
    params:
        perc_identity=95,
        outfmt=6,
        num_threads=2,
        max_target_seqs=1,
        max_hsps=1,
        db_prefix="output/{type}/db/{db}"
    conda:
        "env/env.yaml"
    script:
        "scripts/blastn.py"