snipar.utilities module

class snipar.utilities.NumRangeAction(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)

Bases: Action

flattens and sorts the resulting num range. also removes duplicates

snipar.utilities.convert_str_array(x)

Convert an ascii array to unicode array (UTF-8)

snipar.utilities.coord2linear(ind1: int, ind2: int) → int

snipar.utilities.encode_str_array(x)

Encode a unicode array as an ascii array

snipar.utilities.get_parser_doc(parser)

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

snipar.utilities.make_id_dict(x, col=0)

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

Wrapper of bgen_reader.open_bgen that checks if sample ids make sense.

snipar.utilities.outfile_name(outprefix, outsuffix, chrom=None)

snipar.utilities.parseNumRange(string)

reads either a int or a range

snipar.utilities.parse_filelist(obsfiles, impfiles, obsformat, chromosomes=None)

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

snipar.utilities.read_bgen(filename: str, verbose: bool = False) → Dict

Wrapper of bgen_reader.read_bgen that checks if sample ids make sense.