samples=["P01325", "P01308"]

rule targets:
    input:
        expand("fasta/{sample}.fasta", sample=samples),
        "fusionFasta/allSequences.fasta",
        "mafft/mafft_res.fasta",


rule loadData:
    output:
        "fasta/{sample}.fasta",
    log:
        stdout = "logs/{sample}_wget.stdout",
        stderr = "logs/{sample}_wget.stderr",
    params:
        dirFasta = "fasta",
    threads: 1 
    shell:
        """
          wget --output-file {log.stderr} \
               --directory-prefix {params.dirFasta} \
               https://www.uniprot.org/uniprot/{wildcards.sample}.fasta > {log.stdout}
        """


rule fusionFasta:
    input:
        expand("fasta/{sample}.fasta", sample=samples),
    output:
        "fusionFasta/allSequences.fasta",
    log:
        "logs/fusionData.stderr",
    threads: 1
    shell:
        """
            cat {input} > {output} 2> {log}
        """


rule mafft:
    input: 
        rules.fusionFasta.output,
    output:
        "mafft/mafft_res.fasta",
    log:
        "logs/whichMafft.txt",
    threads: 1
    shell:
        """
            mafft {input} > {output} 2> {log}
        """