| |
| |
| """ |
| Created on Wed Feb 5 05:47:08 2025 |
| |
| """ |
| import jax |
| import jax.numpy as jnp |
| from flax import linen as nn |
| from flax.training.train_state import TrainState |
|
|
| def init_pairhmm_indp_sites( seq_shapes, |
| dummy_t_array, |
| tx, |
| model_init_rngkey, |
| pred_config, |
| tabulate_file_loc, |
| *args, |
| **kwargs |
| ): |
| """ |
| for independent site classses over substitution models |
| """ |
| if not pred_config['load_all']: |
| from latent_class_mixtures.IndpSites import IndpSites as model |
| |
| elif pred_config['load_all']: |
| from latent_class_mixtures.IndpSites import IndpSitesLoadAll as model |
| |
| pairhmm_instance = model(config = pred_config, |
| name = 'IndpSites') |
| |
| |
| |
| |
| |
| if (tabulate_file_loc is not None): |
| tab_fn = nn.tabulate(pairhmm_instance, |
| rngs=model_init_rngkey, |
| console_kwargs = {'soft_wrap':True, |
| 'width':250}) |
| str_out = tab_fn(batch = seq_shapes, |
| t_array = dummy_t_array, |
| sow_flax_intermeds = False, |
| mutable = ['params']) |
| with open(f'{tabulate_file_loc}/PAIRHMM_tabulate.txt','w') as g: |
| g.write(str_out) |
| |
| init_params = pairhmm_instance.init(rngs = model_init_rngkey, |
| batch = seq_shapes, |
| t_array = dummy_t_array, |
| sow_flax_intermeds = False, |
| mutable=['params']) |
| |
| pairhmm_trainstate = TrainState.create( apply_fn=pairhmm_instance.apply, |
| params=init_params, |
| tx=tx ) |
| |
| return pairhmm_trainstate, pairhmm_instance |
|
|
|
|
| |
| def init_pairhmm_transit_mixes( pred_model_type, |
| seq_shapes, |
| dummy_t_array, |
| tx, |
| model_init_rngkey, |
| pred_config, |
| tabulate_file_loc |
| ): |
| """ |
| for pairHMM using mixtures of domains, mixtures of fragments |
| """ |
| if (pred_model_type == 'pairhmm_frag_and_site_classes') and (not pred_config['load_all']): |
| from latent_class_mixtures.FragAndSiteClasses import FragAndSiteClasses as model |
| name = 'FragAndSiteClasses' |
| |
| elif (pred_model_type == 'pairhmm_frag_and_site_classes') and (pred_config['load_all']): |
| from latent_class_mixtures.FragAndSiteClasses import FragAndSiteClassesLoadAll as model |
| name = 'FragAndSiteClasses' |
| |
| elif (pred_model_type == 'pairhmm_nested_tkf') and (not pred_config['load_all']): |
| from latent_class_mixtures.NestedTKF import NestedTKF as model |
| name = 'NestedTKF' |
| |
| elif (pred_model_type == 'pairhmm_nested_tkf') and (pred_config['load_all']): |
| from latent_class_mixtures.NestedTKF import NestedTKFLoadAll as model |
| name = 'NestedTKF' |
| |
| pairhmm_instance = model(config = pred_config, |
| name = name) |
| |
| |
| |
| |
| |
| if (tabulate_file_loc is not None): |
| tab_fn = nn.tabulate(pairhmm_instance, |
| rngs=model_init_rngkey, |
| console_kwargs = {'soft_wrap':True, |
| 'width':250}) |
| str_out = tab_fn(batch = seq_shapes, |
| t_array = dummy_t_array, |
| sow_flax_intermeds = False, |
| mutable = ['params']) |
| with open(f'{tabulate_file_loc}/PAIRHMM_tabulate.txt','w') as g: |
| g.write(str_out) |
| |
| init_params = pairhmm_instance.init(rngs = model_init_rngkey, |
| batch = seq_shapes, |
| t_array = dummy_t_array, |
| sow_flax_intermeds = False, |
| mutable=['params']) |
| |
| pairhmm_trainstate = TrainState.create( apply_fn=pairhmm_instance.apply, |
| params=init_params, |
| tx=tx ) |
| |
| return pairhmm_trainstate, pairhmm_instance |
|
|
