API reference

gwas.py

class gwas.ActionAppendDeprecated(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)

Methods

__call__(parser, namespace, values[, ...])

Call self as a function.

format_usage

class gwas.ActionStoreDeprecated(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)

Methods

__call__(parser, namespace, values[, ...])

Call self as a function.

format_usage

class gwas.LoadFromFile(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)

Methods

__call__(parser, namespace, values[, ...])

Call self as a function.

format_usage

class gwas.Logger(fh, mode)

Lightweight logging.

Methods

error(msg)	Print to log file, error file and stdout with a single command.
log(msg)	Print to log file and stdout with a single command.

error(msg)

Print to log file, error file and stdout with a single command.

log(msg)

Print to log file and stdout with a single command.

class gwas.NumpyEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Methods

default(obj)	Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).
encode(o)	Return a JSON string representation of a Python data structure.
iterencode(o[, _one_shot])	Encode the given object and yield each string representation as available.

default(obj)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return super().default(o)

gwas.sec_to_str(t)

Convert seconds to days:hours:minutes:seconds