Snakefile

# TODO: the results should probably go in a data directory.
blast_output = "../combined_results.txt"
distance_file = "../combined_results_distances.tsv"
graphml_file = "../graph_cluster.graphml"

rule get_sequences:
    output:
        "goodseqs.fasta"
    shell:
        "python preprocessing/get_seqs.py" # TODO: Args

rule blast_all:
    input:
        "goodseqs.fasta"
    output:
        blast_output
    shell:
        "bash blast_all_parallel.sh" #FIXME: output path in script probably doesn't match here

rule compute_distances:
    input:
        blast_output
    output:
        distance_file
    shell:
        "python preprocessing/computedistances.py " +
        "-i {input} -o {output} " +
        "--distance-metric short_hamming " +
        "-f 'qacc sacc length qlen slen pident'"

rule seq_similarity_network:
    input:
        distance_file
    output:
       graphml_file
    shell:
        "Rscript seq_sim_network.R"