def configure(len_size=None,
genomic_distance=None,
methods_name='ours',
dataset_path=None,
raw_path='raw',
raw_hic='Rao2014-GM12878-DpnII-allreps-filtered.10kb.cool',
input_path='input',
output_path='output'):
resolution = None # assigned by cooler binsizes
scale = 4
if len_size is None:
len_size = 40
block_size = 2048 # number of entries in one file
if genomic_distance is None:
genomic_distance = 200000
if dataset_path is None:
# assume current directory is the root of project
# pathto/proj/data
# pathto/proj/our_method
dataset_path = os.path.join(
operations.redircwd_back_projroot(
project_name='refine_resolution'), 'data')
print('data path: ', dataset_path)
input_file = raw_hic.split('-')[0] + '_' + raw_hic.split(
'-')[1] + '_' + raw_hic.split('-')[2] + '_' + raw_hic.split('.')[1]
input_path = '_'.join(
[input_path, methods_name,
str(genomic_distance),
str(len_size)])
output_file = input_file
output_path = '_'.join(
[output_path, methods_name,
str(genomic_distance),
str(len_size)])
# load raw hic matrix
file = os.path.join(dataset_path, raw_path, raw_hic)
print('raw hic data: ', file)
'''if ~os.path.exists(file):
url = 'ftp://cooler.csail.mit.edu/coolers/hg19/'+raw_hic
print(url)
file = wget.download(url, file)'''
cool_hic = cooler.Cooler(file)
resolution = cool_hic.binsize
return cool_hic, resolution, scale, len_size, genomic_distance,\
block_size, dataset_path, \
[raw_path, raw_hic], \
[input_path, input_file], \
[output_path, output_file]
"""
configure data:
dataset_path-raw
-input
-output
"""
if __name__ == '__main__':
raw_list = [
'Rao2014-CH12LX-MboI-allreps-filtered.10kb.cool',
'Rao2014-GM12878-DpnII-allreps-filtered.10kb.cool',
'Rao2014-GM12878-MboI-allreps-filtered.10kb.cool',
'Rao2014-HMEC-MboI-allreps-filtered.10kb.cool',
'Rao2014-HUVEC-MboI-allreps-filtered.10kb.cool',
'Rao2014-IMR90-MboI-allreps-filtered.10kb.cool',
'Rao2014-K562-MboI-allreps-filtered.10kb.cool',
'Rao2014-KBM7-MboI-allreps-filtered.10kb.cool',
'Rao2014-NHEK-MboI-allreps-filtered.10kb.cool'
]
root = operations.redircwd_back_projroot(project_name='refine_resolution')
raw_hic = 'Rao2014-GM12878-MboI-allreps-filtered.10kb.cool'
# raw_hic='Rao2014-GM12878-DpnII-allreps-filtered.10kb.cool'
config = configure(raw_hic=raw_hic,
len_size=int(sys.argv[2]),
genomic_distance=int(sys.argv[3]))
chromosome_list = [str(sys.argv[1])]
for chri in chromosome_list:
save_samples(config, chromosome=chri)
if hic_lr is None:
hic_lr = data['hic']
else:
hic_lr = np.concatenate((hic_lr, data['hic']), axis=0)
return hic_hr, hic_lr
if __name__ == '__main__':
# the size of input
len_size = int(sys.argv[1]) # 40, 128, 200
scale = 4
# genomic_disstance is used for input path, nothing to do with model
genomic_distance = int(sys.argv[2]) # 2000000, 2560000
EPOCHS = 300
BATCH_SIZE = 9
root_path = redircwd_back_projroot(project_name='refine_resolution')
data_path = os.path.join(root_path, 'data')
# raw_hic = 'Rao2014-GM12878-DpnII-allreps-filtered.10kb.cool'
raw_hic = 'Rao2014-GM12878-MboI-allreps-filtered.10kb.cool'
input_path = '_'.join(['input', 'ours', str(genomic_distance), str(len_size)])
input_file = raw_hic.split('-')[0] + '_' + raw_hic.split('-')[1] + '_' + raw_hic.split('-')[2] + '_' + raw_hic.split('.')[1]
log_dir = os.path.join(root_path, 'our_model', 'logs', 'model')
logging.basicConfig(filename=os.path.join(log_dir, 'training.log'), level=logging.INFO)
# ['1', '2', '3', '4', '5','6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16']
# ['17', '18']
# ['19', '20', '21', '22', 'X']
train_chr_list = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16']
valid_chr_list = ['17', '18']