rule all:
    input: 
        "results/alignment/P10415_P01308_aligned.fasta",

rule loadData:
    output:
        "results/data/{sample}.fasta",
    shell:
        """
        wget --directory-prefix $(dirname {output}) \
               https://www.uniprot.org/uniprot/{wildcards.sample}.fasta
        """

rule fusionFasta:
    input:
        p1="results/data/{upid1}.fasta",
        p2="results/data/{upid2}.fasta",
    output:
        "results/alignment/{upid1}_{upid2}_fused.fasta",
    shell:
        """
        cat {input.p1} {input.p2} > {output}
        """
    
rule mafft:
    input:
        "results/alignment/{prefix}_fused.fasta",
    output:
        "results/alignment/{prefix}_aligned.fasta",
    shell:
        """
        mafft {input} > {output}
        """