Mercurial > repos > yating-l > data_manager_fetch_reference_data

comparison data_manager/fetch_reference_data.py @ 6:2eb398f3649c draft

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planemo upload
author yating-l
date Wed, 03 May 2017 17:49:01 -0400
parents 2f926e7d623d
children 83362eed7868
comparison
equal deleted inserted replaced
5:2f926e7d623d 6:2eb398f3649c
44 with tarfile.open(filepath, mode='r:*') as tar: 44 with tarfile.open(filepath, mode='r:*') as tar:
45 subdir = [ 45 subdir = [
46 tarinfo for tarinfo in tar.getmembers() 46 tarinfo for tarinfo in tar.getmembers()
47 if sequence_id in tarinfo.name 47 if sequence_id in tarinfo.name
48 ] 48 ]
49 tar.extractall(members=subdir) 49 tar.extractall(path=downloadpath, members=subdir)
50 GlimmerHMM_TRAINED_DIR = os.path.join(downloadpath, 'GlimmerHMM', 'trained_dir', sequence_id) 50 glimmerhmm_trained_dir = os.path.join(downloadpath, 'GlimmerHMM', 'trained_dir', sequence_id)
51 glimmerhmm_trained_target_dir = os.path.join(target_directory, sequence_id) 51 glimmerhmm_trained_target_dir = os.path.join(target_directory, sequence_id)
52 shutil.copytree(GlimmerHMM_TRAINED_DIR, glimmerhmm_trained_target_dir) 52 shutil.copytree(glimmerhmm_trained_dir, glimmerhmm_trained_target_dir)
53 data_table_entry = dict(value=sequence_id, name=sequence_name, path=glimmerhmm_trained_target_dir) 53 data_table_entry = dict(value=sequence_id, name=sequence_name, path=glimmerhmm_trained_target_dir)
54 _add_data_table_entry(data_manager_dict, data_table_entry) 54 _add_data_table_entry(data_manager_dict, data_table_entry)
55 55
56 cleanup_before_exit('tmp') 56 cleanup_before_exit('tmp')
57 57