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

Classes

`PostProcessing`	Class that can do PostProcessing of HAPSBURG output.
`NoPostProcessing`	Class that does no Postprocessing
`IBD2Postprocessing`	Class that can do PostProcessing of HAPSBURG output.

Functions

load_Postprocessing([p_model])

Factory Method for PostProcessing class

Module Contents

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