"""Download the required files

"""

from bpnet.dataspecs import DataSpec

base_url = 'http://mitra.stanford.edu/kundaje/avsec/chipnexus/paper/data'

dataspecs = ['chip-nexus/dataspec.yml',

             'chip-seq/dataspec.yml']

# download all the required files by the DataSpec to ./data

rule all:

    input:

        [os.path.normpath(os.path.join('data', f))

         for ds in dataspecs

         for f in DataSpec.load(ds).list_all_files(include_peaks=True)],

        "data/mm10.subset.fa"

rule chip_nexus:

    input:

        [os.path.normpath(os.path.join('data', f))

         for f in DataSpec.load('chip-nexus/dataspec.yml').list_all_files(include_peaks=True)]

rule chip_seq:

    input:

        [os.path.normpath(os.path.join('data', f))

         for f in DataSpec.load('chip-nexus/dataspec.yml').list_all_files(include_peaks=True)]

# -----------------------

rule download:

    """Download an individual file

    """

    output:

        f = 'data/{tf}/{path}'

    params:

        base_url = base_url

    shell:

        "wget {params.base_url}/{wildcards.tf}/{wildcards.path} -O {output.f}"

rule download_fasta:

    """Download an individual file

    """

    output:

        f = 'data/mm10.subset.fa.gz'

    params:

        base_url = base_url

    shell:

        "wget {params.base_url}/mm10.subset.fa.gz -O {output.f}"

# extract the fasta file

rule unzip:

    input:

        f = "{path}.fa.gz"

    output:

        f = "{path}.fa"

    shell:

        "zcat {input.f} > {output.f}"