ancIBD.main
ancIBD: Main HMM class. Pulls together other ancIBD modules and directs loading/running them. @author: Harald Ringbauer, 2020
Module Contents
Classes
Analyze Class for HMMs. Wrapper for various subclasses, making them |
- class ancIBD.main.HMM_Full(folder_in='', l_model='simulated', t_model='standard', e_model='haploid_gl', h_model='FiveStateFast', p_model='hapROH', output=True, load=True)
Bases:
objectAnalyze Class for HMMs. Wrapper for various subclasses, making them work together. Contains objects as field for pre-processing, transition as well as emission probabilities, loading and post-processing Contains most Parameters (but some of them like the output folders are decided by pre-processing subclass)
- folder_in = ''
- folder_out = ''
- l_model = ''
- e_model = ''
- t_model = ''
- p_model = ''
- h_model = ''
- post_model = ''
- fwd_bwd = 0
- submat33 = True
- in_val = 0.0001
- output = True
- load_objects()
Load all the required Objects in right order
- run_fwd_bwd(full=True)
Run Forward Backward algorithm.
- run_fwd_bwd_timed(full=True)
Run Forward Backward algorithm. Legacy: Timed version.
- set_params(**kwargs)
Set the Parameters. Takes keyworded arguments
- prepare_path(base_path, ch, prefix_out='', logfile=False)
Prepare the output path and pipe printing for one Individual. Create Path if not already existing. prefix_out: Optional additonal folder. logfile: Whether to pipe output to log-file [WARNING: This is an ugly hack]
- reset_print()
Resets output to console.