`ancIBD.IO.h5_load`

Functions to load data from a HDF5 file @ Author: Harald Ringbauer, 2021

Module Contents

`get_idx_iid`(f, sample[, unique])	Return Index of sample samples in hdf5 f
`get_idx_iid_exact`(f, sample[, unique])	Return Index of sample samples in hdf5 f
`get_coverage`(f, j)	Get Coverage of sample j in hdf5 f
`get_markers_good`(f, j[, output, cutoff, ploidy])	Get markers
`get_genos`(f[, iid, min_gp, output, phased, exact])	Return Genotypes and Map of pairs at intersection with GP>cutoff.
`load_individual_h5`([path_h5, min_gp, chs, iid, output])	Load individual data from set of chromosomal hdf5s.
`get_genos_pairs`(f[, sample1, sample2, cutoff, output, ...])	Return Genotypes and Map of pairs at intersection with GP>cutoff.
`opp_homos`(g1, g2)	Return opposing homozygotes
`get_opp_homos_f`([f_path, iid1, iid2, ch, cutoff, ...])	Return opposing homozygotes boolean array and map array at intersection with
`get_opp_homos_X`(f_path, iid1, iid2[, ploidy, cutoff, ...])	return oppo homo boolean array and map array at intersection with GP>cutoff. This function is tailored for X chromosome.
`get_diff_gt_f`(f_path, iid1, iid2, ch[, cutoff, ...])	Return diff genotype boolean array and map array at intersection of maxGP > cutoff

ancIBD.IO.h5_load.get_idx_iid(f, sample, unique=True): Return Index of sample samples in hdf5 f

ancIBD.IO.h5_load.get_idx_iid_exact(f, sample, unique=True): Return Index of sample samples in hdf5 f

ancIBD.IO.h5_load.get_markers_good(f, j, output=True, cutoff=0.99, ploidy=2): Get markers

ancIBD.IO.h5_load.get_genos(f, iid='SUC002', min_gp=0.98, output=True, phased=False, exact=True): Return Genotypes and Map of pairs at intersection with GP>cutoff. phased: Whether to return [lx2] phased vector or [l] vetor of #derived. exact: Whether IID has to be an exact match

ancIBD.IO.h5_load.load_individual_h5(path_h5='/n/groups/reich/hringbauer/git/hapBLOCK/data/hdf5/1240k_v43/ch', min_gp=0.98, chs=range(1, 23), iid='SUC002', output=False): Load individual data from set of chromosomal hdf5s.

ancIBD.IO.h5_load.get_genos_pairs(f, sample1='SUC006', sample2='R26.SG', cutoff=0.98, output=True, phased=False, exact=False, ploidy=(2, 2)): Return Genotypes and Map of pairs at intersection with GP>cutoff. phased: Whether to return [lx2] phased vector or [l] vetor of #derived. exact: Whether IID has to be an exact match

ancIBD.IO.h5_load.get_opp_homos_f(f_path='/n/groups/reich/hringbauer/git/hapBLOCK/data//hdf5/1240k_v43/ch', iid1='SUC006', iid2='R26.SG', ch=3, cutoff=0.99, output=True, exact=False): Return opposing homozygotes boolean array and map array at intersection with GP>cutoff.

ancIBD.IO.h5_load.get_opp_homos_X(f_path, iid1, iid2, ploidy=(2, 2), cutoff=0.99, output=True, exact=False): return oppo homo boolean array and map array at intersection with GP>cutoff. This function is tailored for X chromosome. Be careful with the ploidy difference between males and females. The ploidy argument should be a tuple of two integers, indicating the ploidy of iid1, iid2, respectively.

ancIBD.IO.h5_load.get_diff_gt_f(f_path, iid1, iid2, ch, cutoff=0.99, output=True, exact=False): Return diff genotype boolean array and map array at intersection of maxGP > cutoff