__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

# Samtools takes additional threads through its option -@
# One thread for samtools merge
# Other threads are *additional* threads passed to the '-@' argument
threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)

shell(
    "samtools index {threads} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
)

run:
    with open(output[0], "w") as out:
        with open (input[0], "r") as inp:
            i = 1
            for line in inp:
                if line.startswith(">"):
                    line = ">id_" + str(i) + "\n"
                    i += 1 
                out.write(line)

wrapper: "v1.12.2/bio/bowtie2/build"

wrapper: "v1.12.2/bio/bowtie2/align"

shell:
    "(samtools view -h {input} | {workflow.basedir}/scripts/read_count_bam.pl | samtools view -Su -q30 - | samtools sort -O BAM -o {output} -) 2>> {log}"

wrapper: "v1.12.2/bio/samtools/index"

shell:
    """
    echo '#OTU ID' > {output}
    samtools idxstats $(ls {input.bam} | head -n 1) | grep -v "*" | cut -f1 >> {output}
    """

shell:
    """
    echo '{wildcards.sample}' > {output}
    samtools idxstats {input.bam} | grep -v "*" | cut -f3 >> {output}
    """

shell:
    """
    cp {input.ids} {output}
    # split if exceed 1000 (max 1024 by default in most OS)
    while read fs; do
        paste {output} $fs > {output}.tmp
        # redirection first
        mv {output}.tmp {output}
    done < <(echo {input.counts} | xargs -n 1000)
    """

shell: "samtools dict {input} | cut -f1-3 > {output} 2> {log}"

shell:
    """
    minimap2 -t {threads} -ax {params.x} --secondary=no {input.mmi} {input.fq} 2> {log} | \
    grep -v "^@" | cat {input.dict} - > {output} 2>> {log}
    """

shell:
    "samtools view -F 3584 -b {input} | samtools sort - -T {params.prefix} -m {params.m} -o {output} 2>{log}"