How to use the kipoi.specs.RemoteFile function in kipoi
To help you get started, we’ve selected a few kipoi examples, based on popular ways it is used in public projects.
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kipoi / models / FactorNet / GABPA / meta_RNAseq_Unique35_DGF / dataloader.py View on Github 
"""
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)
"""
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)
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"""
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)
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 = [
("cpg", BedTool(gp + '/cpgisland.bed.gz')),"""
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)
"""
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)
"""
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)
Popular kipoi functions
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- kipoi.specs.Author
- kipoi.specs.DataLoaderArgument
- kipoi.specs.Dependencies
- kipoi.specs.RemoteFile
- kipoi.utils.load_module
- kipoi.utils.makedir_exist_ok
- kipoi.utils.read_txt