snipar.utilities module

snipar.utilities.convert_str_array(x)[source]: Convert an ascii array to unicode array (UTF-8)

snipar.utilities.coord2linear(ind1: int, ind2: int) → int[source]

snipar.utilities.encode_str_array(x)[source]: Encode a unicode array as an ascii array

snipar.utilities.get_parser_doc(parser)[source]

snipar.utilities.linear2coord(ind: int) → Tuple[int, int][source]

snipar.utilities.make_id_dict(x, col=0)[source]: Make a dictionary that maps from the values in the given column (col) to their row-index in the input array

snipar.utilities.open_bgen(filename: str, verbose: bool = False) → open_bgen[source]: Wrapper of bgen_reader.open_bgen that checks if sample ids make sense.

snipar.utilities.outfile_name(outprefix, outsuffix, chrom=None)[source]

snipar.utilities.parse_filelist(obsfiles, impfiles, obsformat, chromosomes=None)[source]

snipar.utilities.parse_obsfiles(obsfiles, obsformat='bed', append=True, wildcard='@', chromosomes=None)[source]

snipar.utilities.read_bgen(filename: str, verbose: bool = False) → Dict[source]: Wrapper of bgen_reader.read_bgen that checks if sample ids make sense.