ancIBD.postprocessing
Class for calling IBD from Posterior Data. Saves results as tab seperated .tsv created by Pandas and Numpy Contains Sub-Classes, as well as factory Method. Pls always change parameters with set_params method! @ Author: Harald Ringbauer, 2020
Module Contents
Classes
Class that can do PostProcessing of HAPSBURG output. |
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Class that does no Postprocessing |
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Class that can do PostProcessing of HAPSBURG output. |
Functions
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Factory Method for PostProcessing class |
- class ancIBD.postprocessing.PostProcessing(folder='')
Bases:
object
Class that can do PostProcessing of HAPSBURG output. (for one individual). Sometimes post-processing is done outside that, Has Methods to save the output. Saves using standard hapROH format
- folder = ''
- cutoff_post = 0.99
- min_cm = 4
- max_gap = 0.01
- save = 0
- output = True
- ch = 3
- iid = 'iid0'
- mask = ''
- set_params(**kwargs)
Set the Parameters. Takes keyworded arguments
- roh_posterior(posterior0)
Calculate the IBD posterior. Input: Posterior 0 [l] Output: 1 - Posterior 0 [l]
- ibd_stat_to_block(ibd)
Convert IBD status per marker into list of ibd. Input: IBD stats [l] boolean. Return start and end indexes of IBD blocks
- create_df(starts, ends, starts_map, ends_map, l, l_map, ch, starts_bp, ends_bp, min_cm, iid1, iid2='')
Create and returndthe hapBLOCK/hapROH dataframe.
- merge_called_blocks(df, max_gap=0)
Merge Blocks in Dataframe df and return merged Dataframe
- save_output(df, r_map=[], post=[], save_folder='')
Save hapBLOCK output in standardized format.
- save_ibd_df(df_ibd, save_path)
Save IBD Dataframe to path save_path
- mask_regions(df)
- call_roh(r_map, bp, post0, iid1='', iid2='')
Call ROH of Homozygosity from Posterior Data bigger than cutoff. post0: posterior in format [5,l], log space
- class ancIBD.postprocessing.NoPostProcessing(folder='')
Bases:
PostProcessing
Class that does no Postprocessing
- call_roh(**kwd)
Does nothing
- class ancIBD.postprocessing.IBD2Postprocessing(folder='')
Bases:
PostProcessing
Class that can do PostProcessing of HAPSBURG output. (for one individual). Sometimes post-processing is done outside that, Has Methods to save the output. Saves using standard hapROH format
- min_cm2_init = 1.0
- min_cm2_after_merge = 2.0
- cutoff_post1 = 0.99
- cutoff_post2 = 0.975
- create_df(starts, ends, starts_map, ends_map, l, l_map, starts_bp, ends_bp, ch, min_cm, iid1, iid2, segment_type='IBD1')
Create and returndthe hapBLOCK/hapROH dataframe.
- get_posterior(post0)
- call_roh(r_map, bp, post0, iid1='', iid2='')
Call ROH of Homozygosity from Posterior Data bigger than cutoff. post0: posterior in format [7,l], log space
- ancIBD.postprocessing.load_Postprocessing(p_model='hapROH')
Factory Method for PostProcessing class