default_config.py

default_config = \
    {'exp_name': '',
     'data_dir': '',
     'summary_dir': 'summary',
     'model_dir': 'model',
     'distance_mode': 'L2',
     'embedding_size': -1,
     'sequence_length': 0,
     'h_channel': 8,
     'beta_ratio': 50000,

     'tau_pres_end_epoch': 5,
     'start_epoch': 0,
     'epoch': 3001,
     'batch_size': 32,
     'cp': 1.0,
     'resblock_num': 1,

     'lr': 2e-4,
     'lr_decay': 2000,
     'backbone_tree_file': '',
     'backbone_seq_file': '',
     'query_seq_file': '',
     'weighted_method': 'square_root_fm',
     'distance_alpha': 1e7,
     'dis_loss_ratio': 1.0,
     'plot_freq': 1000,
     'save_data_freq': 1000,
     'save_model_freq': 3000,
     'print_freq': 1000,
     'stop_par': 200,
     'gpus': [0],
     'plot_all_freqdistance_depp.sh -q ./seq/query_seq/query_seq.fa -b ./seq/backbone_seq/backbone_seq.fa -m model/epoch\=599.ckpt -t tree/backbone_tree/backbone.newick -o dis_mat/': 2000,
     'lr_update_freq': 100,
     'bar_update_freq': 1,
     'val_freq': 50,
     'patience': 5,
     'model_path': '',
     'outdir': 'depp_distance',
     'num_worker': 4,
     'replicate_seq': False,
     'gap_encode': 0,
     'jc_correct': False,
     'k': 1.0,
     'ratio': 1,
     'internal': False
     }

# def get_cfg_defaults():
#    """Get a yacs CfgNode object with default values for my_project."""
#    # Return a clone so that the defaults will not be altered
#    # This is for the "local variable" use pattern
#    return _C.clone()