How to use the kipoi.utils.makedir_exist_ok function in kipoi

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github kipoi / models / FactorNet / REST / GENCODE_Unique35_DGF_2 / dataloader.py View on Github external
else:
            BT = BedTool

        self.bt = BT(intervals_file)

        # Fasta
        self.fasta_file = fasta_file
        self.fasta_extractor = None  # initialize later
        # DNase
        self.dnase_file = dnase_file
        self.dnase_extractor = None
        # mappability
        if mappability_file is None:
            # download the mappability file if not existing
            common_dl_dir = os.path.join(this_dir, "../../template/downloaded/dataloader_files")
            makedir_exist_ok(common_dl_dir)
            rf = RemoteFile(url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness35bp.bigWig",
                            md5="1d15ddafe2c8df51cf08495db96679e7")
            mappability_file = os.path.join(common_dl_dir, "wgEncodeDukeMapabilityUniqueness35bp.bigWig")
            if not os.path.exists(mappability_file) or not rf.validate(mappability_file):
                # download the path
                rf.get_file(mappability_file)
        self.mappability_file = mappability_file
        self.mappability_extractor = None
        # Gencode features
        if GENCODE_dir is None:
            gp = os.path.join(this_dir, "../../template/downloaded/dataloader_files/gencode_features/")
        else:
            gp = GENCODE_dir

        download_gencode_dir(gp)  # download files
        self.gencode_beds = [
github kipoi / models / FactorNet / GABPA / meta_RNAseq_Unique35_DGF / dataloader.py View on Github external
else:
            BT = BedTool

        self.bt = BT(intervals_file)

        # Fasta
        self.fasta_file = fasta_file
        self.fasta_extractor = None  # initialize later
        # DNase
        self.dnase_file = dnase_file
        self.dnase_extractor = None
        # mappability
        if mappability_file is None:
            # download the mappability file if not existing
            common_dl_dir = os.path.join(this_dir, "../../template/downloaded/dataloader_files")
            makedir_exist_ok(common_dl_dir)
            rf = RemoteFile(url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness35bp.bigWig",
                            md5="1d15ddafe2c8df51cf08495db96679e7")
            mappability_file = os.path.join(common_dl_dir, "wgEncodeDukeMapabilityUniqueness35bp.bigWig")
            if not os.path.exists(mappability_file) or not rf.validate(mappability_file):
                # download the path
                rf.get_file(mappability_file)
        self.mappability_file = mappability_file
        self.mappability_extractor = None
        # Get the metadata features
        if cell_line is None:
            if RNAseq_PC_file is None:
                raise ValueError("RNAseq_PC_file has to be specified when cell_line=None")
            assert os.path.exists(RNAseq_PC_file)
        else:
            # Using the pre-defined cell-line
            output_dir = os.path.join(this_dir, "../../template/downloaded/dataloader_files/RNAseq_features/")
github kipoi / models / FactorNet / REST / GENCODE_Unique35_DGF_2 / dataloader.py View on Github external
def download_gencode_dir(output_dir):
    """Download all the required gencode files
    """
    makedir_exist_ok(output_dir)

    url_template = ("https://s3.eu-central-1.amazonaws.com/kipoi-models/"
                    "dataloader_files/FactorNet/dataloader_files/gencode_features/{}")

    # url_template = "https://github.com/uci-cbcl/FactorNet/blob/master/resources/{}?raw=true"
    fnames = [('cpgisland.bed.gz', 'ac7dc007d7019c05adb7a331d1d6721d'),
              ('wgEncodeGencodeBasicV19.cds.merged.bed.gz', '4ec9883932932efe87e4adc6c84ced1c'),
              ('wgEncodeGencodeBasicV19.intron.merged.bed.gz', 'd2db7e3255323d2b5b04e1c0c59ecd2d'),
              ('wgEncodeGencodeBasicV19.promoter.merged.bed.gz', '48fe1ab3aa0e9f5d11f3e5dfedbd47b6'),
              ('wgEncodeGencodeBasicV19.utr5.merged.bed.gz', 'de87c14d4ff055226afeb01446aba6e6'),
              ('wgEncodeGencodeBasicV19.utr3.merged.bed.gz', '8bbe08f5fba86306dfbef56d756856f1')]
    for fname, md5 in fnames:
        output_file = os.path.join(output_dir, fname)
        rf = RemoteFile(url=url_template.format(fname), md5=md5)
        if not os.path.exists(output_file) or not rf.validate(output_file):
            rf.get_file(output_file)
github kipoi / models / FactorNet / FOXA1 / multiTask_DGF / dataloader.py View on Github external
def download_gencode_dir(output_dir):
    """Download all the required gencode files
    """
    makedir_exist_ok(output_dir)

    url_template = ("https://s3.eu-central-1.amazonaws.com/kipoi-models/"
                    "dataloader_files/FactorNet/dataloader_files/gencode_features/{}")

    # url_template = "https://github.com/uci-cbcl/FactorNet/blob/master/resources/{}?raw=true"
    fnames = [('cpgisland.bed.gz', 'ac7dc007d7019c05adb7a331d1d6721d'),
              ('wgEncodeGencodeBasicV19.cds.merged.bed.gz', '4ec9883932932efe87e4adc6c84ced1c'),
              ('wgEncodeGencodeBasicV19.intron.merged.bed.gz', 'd2db7e3255323d2b5b04e1c0c59ecd2d'),
              ('wgEncodeGencodeBasicV19.promoter.merged.bed.gz', '48fe1ab3aa0e9f5d11f3e5dfedbd47b6'),
              ('wgEncodeGencodeBasicV19.utr5.merged.bed.gz', 'de87c14d4ff055226afeb01446aba6e6'),
              ('wgEncodeGencodeBasicV19.utr3.merged.bed.gz', '8bbe08f5fba86306dfbef56d756856f1')]
    for fname, md5 in fnames:
        output_file = os.path.join(output_dir, fname)
        rf = RemoteFile(url=url_template.format(fname), md5=md5)
        if not os.path.exists(output_file) or not rf.validate(output_file):
            rf.get_file(output_file)
github kipoi / models / FactorNet / TAF1 / onePeak_Unique35_DGF / dataloader.py View on Github external
else:
            BT = BedTool

        self.bt = BT(intervals_file)

        # Fasta
        self.fasta_file = fasta_file
        self.fasta_extractor = None  # initialize later
        # DNase
        self.dnase_file = dnase_file
        self.dnase_extractor = None
        # mappability
        if mappability_file is None:
            # download the mappability file if not existing
            common_dl_dir = os.path.join(this_dir, "../../template/downloaded/dataloader_files")
            makedir_exist_ok(common_dl_dir)
            rf = RemoteFile(url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness35bp.bigWig",
                            md5="1d15ddafe2c8df51cf08495db96679e7")
            mappability_file = os.path.join(common_dl_dir, "wgEncodeDukeMapabilityUniqueness35bp.bigWig")
            if not os.path.exists(mappability_file) or not rf.validate(mappability_file):
                # download the path
                rf.get_file(mappability_file)
        self.mappability_file = mappability_file
        self.mappability_extractor = None
github kipoi / models / FactorNet / NANOG / GENCODE_Unique35_DGF / dataloader.py View on Github external
def download_gencode_dir(output_dir):
    """Download all the required gencode files
    """
    makedir_exist_ok(output_dir)

    url_template = ("https://s3.eu-central-1.amazonaws.com/kipoi-models/"
                    "dataloader_files/FactorNet/dataloader_files/gencode_features/{}")

    # url_template = "https://github.com/uci-cbcl/FactorNet/blob/master/resources/{}?raw=true"
    fnames = [('cpgisland.bed.gz', 'ac7dc007d7019c05adb7a331d1d6721d'),
              ('wgEncodeGencodeBasicV19.cds.merged.bed.gz', '4ec9883932932efe87e4adc6c84ced1c'),
              ('wgEncodeGencodeBasicV19.intron.merged.bed.gz', 'd2db7e3255323d2b5b04e1c0c59ecd2d'),
              ('wgEncodeGencodeBasicV19.promoter.merged.bed.gz', '48fe1ab3aa0e9f5d11f3e5dfedbd47b6'),
              ('wgEncodeGencodeBasicV19.utr5.merged.bed.gz', 'de87c14d4ff055226afeb01446aba6e6'),
              ('wgEncodeGencodeBasicV19.utr3.merged.bed.gz', '8bbe08f5fba86306dfbef56d756856f1')]
    for fname, md5 in fnames:
        output_file = os.path.join(output_dir, fname)
        rf = RemoteFile(url=url_template.format(fname), md5=md5)
        if not os.path.exists(output_file) or not rf.validate(output_file):
            rf.get_file(output_file)
github kipoi / models / FactorNet / NANOG / GENCODE_Unique35_DGF / dataloader.py View on Github external
else:
            BT = BedTool

        self.bt = BT(intervals_file)

        # Fasta
        self.fasta_file = fasta_file
        self.fasta_extractor = None  # initialize later
        # DNase
        self.dnase_file = dnase_file
        self.dnase_extractor = None
        # mappability
        if mappability_file is None:
            # download the mappability file if not existing
            common_dl_dir = os.path.join(this_dir, "../../template/downloaded/dataloader_files")
            makedir_exist_ok(common_dl_dir)
            rf = RemoteFile(url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness35bp.bigWig",
                            md5="1d15ddafe2c8df51cf08495db96679e7")
            mappability_file = os.path.join(common_dl_dir, "wgEncodeDukeMapabilityUniqueness35bp.bigWig")
            if not os.path.exists(mappability_file) or not rf.validate(mappability_file):
                # download the path
                rf.get_file(mappability_file)
        self.mappability_file = mappability_file
        self.mappability_extractor = None
        # Gencode features
        if GENCODE_dir is None:
            gp = os.path.join(this_dir, "../../template/downloaded/dataloader_files/gencode_features/")
        else:
            gp = GENCODE_dir

        download_gencode_dir(gp)  # download files
        self.gencode_beds = [
github kipoi / models / FactorNet / GABPA / meta_RNAseq_Unique35_DGF / dataloader.py View on Github external
md5="1d15ddafe2c8df51cf08495db96679e7")
            mappability_file = os.path.join(common_dl_dir, "wgEncodeDukeMapabilityUniqueness35bp.bigWig")
            if not os.path.exists(mappability_file) or not rf.validate(mappability_file):
                # download the path
                rf.get_file(mappability_file)
        self.mappability_file = mappability_file
        self.mappability_extractor = None
        # Get the metadata features
        if cell_line is None:
            if RNAseq_PC_file is None:
                raise ValueError("RNAseq_PC_file has to be specified when cell_line=None")
            assert os.path.exists(RNAseq_PC_file)
        else:
            # Using the pre-defined cell-line
            output_dir = os.path.join(this_dir, "../../template/downloaded/dataloader_files/RNAseq_features/")
            makedir_exist_ok(output_dir)
            RNAseq_PC_file = os.path.join(output_dir, cell_line, "meta.txt")
            url_template = ('https://s3.eu-central-1.amazonaws.com/kipoi-models/dataloader_files/'
                            'FactorNet/dataloader_files/RNAseq_features/{}/meta.txt')
            # rf = RemoteFile(url=url_template.format(cell_line))
            if not os.path.exists(RNAseq_PC_file):  # or not rf.validate(mappability_file):
                # download the path
                download_url(url_template.format(cell_line), os.path.join(output_dir, cell_line), "meta.txt")
                # rf.get_file(RNAseq_PC_file)

        self.meta_feat = pd.read_csv(RNAseq_PC_file,
                                     sep="\t", header=None)[0].values