Core language functions¶

`literal`(x, dtype, str, None] = None)	Captures and broadcasts a Python variable or object as an expression.
`cond`(condition, consequent, alternate, …)	Deprecated in favor of `if_else()`.
`if_else`(condition, consequent, alternate, …)	Expression for an if/else statement; tests a condition and returns one of two options based on the result.
`switch`(expr)	Build a conditional tree on the value of an expression.
`case`(missing_false)	Chain multiple if-else statements with a `CaseBuilder`.
`bind`(f, *exprs[, _ctx])	Bind a temporary variable and use it in a function.
`rbind`(*exprs[, _ctx])	Bind a temporary variable and use it in a function.
`null`(t, str])	Creates an expression representing a missing value of a specified type.
`str`(x)	Returns the string representation of x.
`is_missing`(expression)	Returns `True` if the argument is missing.
`is_defined`(expression)	Returns `True` if the argument is not missing.
`coalesce`(*args)	Returns the first non-missing value of args.
`or_else`(a, b)	If a is missing, return b.
`or_missing`(predicate, value)	Returns value if predicate is `True`, otherwise returns missing.
`range`(start[, stop, step])	Returns an array of integers from start to stop by step.

hail.expr.functions.literal(x: Any, dtype: Union[hail.expr.types.HailType, str, None] = None)[source]¶

Captures and broadcasts a Python variable or object as an expression.

Examples

>>> table = hl.utils.range_table(8)
>>> greetings = hl.literal({1: 'Good morning', 4: 'Good afternoon', 6 : 'Good evening'})
>>> table.annotate(greeting = greetings.get(table.idx)).show()
+-------+------------------+
|   idx | greeting         |
+-------+------------------+
| int32 | str              |
+-------+------------------+
|     0 | NA               |
|     1 | "Good morning"   |
|     2 | NA               |
|     3 | NA               |
|     4 | "Good afternoon" |
|     5 | NA               |
|     6 | "Good evening"   |
|     7 | NA               |
+-------+------------------+

Notes

Use this function to capture large Python objects for use in expressions. This function provides an alternative to adding an object as a global annotation on a Table or MatrixTable.

Parameters:	x – Object to capture and broadcast as an expression.
Returns:	`Expression`

hail.expr.functions.cond(condition, consequent, alternate, missing_false: bool = False)[source]¶

Deprecated in favor of if_else().

Expression for an if/else statement; tests a condition and returns one of two options based on the result.

Examples

>>> x = 5
>>> hl.eval(hl.cond(x < 2, 'Hi', 'Bye'))
'Bye'

>>> a = hl.literal([1, 2, 3, 4])
>>> hl.eval(hl.cond(hl.len(a) > 0, 2.0 * a, a / 2.0))
[2.0, 4.0, 6.0, 8.0]

Notes

If condition evaluates to True, returns consequent. If condition evaluates to False, returns alternate. If predicate is missing, returns missing.

Note

The type of consequent and alternate must be the same.

Parameters:	condition (`BooleanExpression`) – Condition to test. consequent (`Expression`) – Branch to return if the condition is `True`. alternate (`Expression`) – Branch to return if the condition is `False`. missing_false (`bool`) – If `True`, treat missing condition as `False`.

See also

case(), switch(), if_else()

Returns:	`Expression` – One of consequent, alternate, or missing, based on condition.

hail.expr.functions.if_else(condition, consequent, alternate, missing_false: bool = False)[source]¶

Expression for an if/else statement; tests a condition and returns one of two options based on the result.

Examples

>>> x = 5
>>> hl.eval(hl.if_else(x < 2, 'Hi', 'Bye'))
'Bye'

>>> a = hl.literal([1, 2, 3, 4])
>>> hl.eval(hl.if_else(hl.len(a) > 0, 2.0 * a, a / 2.0))
[2.0, 4.0, 6.0, 8.0]

Notes

If condition evaluates to True, returns consequent. If condition evaluates to False, returns alternate. If predicate is missing, returns missing.

Note

The type of consequent and alternate must be the same.

Parameters:	condition (`BooleanExpression`) – Condition to test. consequent (`Expression`) – Branch to return if the condition is `True`. alternate (`Expression`) – Branch to return if the condition is `False`. missing_false (`bool`) – If `True`, treat missing condition as `False`.

See also

case(), switch()

Returns:	`Expression` – One of consequent, alternate, or missing, based on condition.

hail.expr.functions.switch(expr) → hail.expr.builders.SwitchBuilder[source]¶

Build a conditional tree on the value of an expression.

Examples

>>> csq = hl.literal('loss of function')
>>> expr = (hl.switch(csq)
...                  .when('synonymous', 1)
...                  .when('SYN', 1)
...                  .when('missense', 2)
...                  .when('MIS', 2)
...                  .when('loss of function', 3)
...                  .when('LOF', 3)
...                  .or_missing())
>>> hl.eval(expr)
3

See also

SwitchBuilder, case(), cond()

Parameters:	expr (`Expression`) – Value to match against.
Returns:	`SwitchBuilder`

hail.expr.functions.case(missing_false: bool = False) → hail.expr.builders.CaseBuilder[source]¶

Chain multiple if-else statements with a CaseBuilder.

Examples

>>> x = hl.literal('foo bar baz')
>>> expr = (hl.case()
...                  .when(x[:3] == 'FOO', 1)
...                  .when(hl.len(x) == 11, 2)
...                  .when(x == 'secret phrase', 3)
...                  .default(0))
>>> hl.eval(expr)
2

Parameters:	missing_false (`bool`) – Treat missing predicates as `False`.

See also

CaseBuilder, switch(), cond()

Returns:	`CaseBuilder`.

hail.expr.functions.bind(f: Callable, *exprs, _ctx=None)[source]¶

Bind a temporary variable and use it in a function.

Examples

>>> hl.eval(hl.bind(lambda x: x + 1, 1))
2

bind() also can take multiple arguments:

>>> hl.eval(hl.bind(lambda x, y: x / y, x, x))
1.0

Parameters:	f (function ( (args) -> `Expression`)) – Function of exprs. exprs (variable-length args of `Expression`) – Expressions to bind.
Returns:	`Expression` – Result of evaluating f with exprs as arguments.

hail.expr.functions.rbind(*exprs, _ctx=None)[source]¶

Bind a temporary variable and use it in a function.

This is bind() with flipped argument order.

Examples

>>> hl.eval(hl.rbind(1, lambda x: x + 1))
2

rbind() also can take multiple arguments:

>>> hl.eval(hl.rbind(4.0, 2.0, lambda x, y: x / y))
2.0

Parameters:	exprs (variable-length args of `Expression`) – Expressions to bind. f (function ( (args) -> `Expression`)) – Function of exprs.
Returns:	`Expression` – Result of evaluating f with exprs as arguments.

hail.expr.functions.null(t: Union[hail.expr.types.HailType, str])[source]¶

Creates an expression representing a missing value of a specified type.

Examples

>>> hl.eval(hl.null(hl.tarray(hl.tstr)))
None

>>> hl.eval(hl.null('array<str>'))
None

Notes

This method is useful for constructing an expression that includes missing values, since None cannot be interpreted as an expression.

Parameters:	t (`str` or `HailType`) – Type of the missing expression.
Returns:	`Expression` – A missing expression of type t.

hail.expr.functions.str(x) → hail.expr.expressions.typed_expressions.StringExpression[source]¶

Returns the string representation of x.

Examples

>>> hl.eval(hl.str(hl.struct(a=5, b=7)))
'{"a":5,"b":7}'

Parameters:	x
Returns:	`StringExpression`

hail.expr.functions.is_missing(expression) → hail.expr.expressions.typed_expressions.BooleanExpression[source]¶

Returns True if the argument is missing.

Examples

>>> hl.eval(hl.is_missing(5))
False

>>> hl.eval(hl.is_missing(hl.null(hl.tstr)))
True

>>> hl.eval(hl.is_missing(hl.null(hl.tbool) & True))
True

Parameters:	expression – Expression to test.
Returns:	`BooleanExpression` – `True` if expression is missing, `False` otherwise.

hail.expr.functions.is_defined(expression) → hail.expr.expressions.typed_expressions.BooleanExpression[source]¶

Returns True if the argument is not missing.

Examples

>>> hl.eval(hl.is_defined(5))
True

>>> hl.eval(hl.is_defined(hl.null(hl.tstr)))
False

>>> hl.eval(hl.is_defined(hl.null(hl.tbool) & True))
False

Parameters:	expression – Expression to test.
Returns:	`BooleanExpression` – `True` if expression is not missing, `False` otherwise.

hail.expr.functions.coalesce(*args)[source]¶

Returns the first non-missing value of args.

Examples

>>> x1 = hl.null('int')
>>> x2 = 2
>>> hl.eval(hl.coalesce(x1, x2))
2

Notes

All arguments must have the same type, or must be convertible to a common type (all numeric, for instance).

See also

or_else()

Parameters:	args (variable-length args of `Expression`)
Returns:	`Expression`

hail.expr.functions.or_else(a, b)[source]¶

If a is missing, return b.

Examples

>>> hl.eval(hl.or_else(5, 7))
5

>>> hl.eval(hl.or_else(hl.null(hl.tint32), 7))
7

See also

coalesce()

Parameters:	a (`Expression`) b (`Expression`)
Returns:	`Expression`

hail.expr.functions.or_missing(predicate, value)[source]¶

Returns value if predicate is True, otherwise returns missing.

Examples

>>> hl.eval(hl.or_missing(True, 5))
5

>>> hl.eval(hl.or_missing(False, 5))
None

Parameters:	predicate (`BooleanExpression`) value (`Expression`) – Value to return if predicate is `True`.
Returns:	`Expression` – This expression has the same type as b.

hail.expr.functions.range(start, stop=None, step=1) → hail.expr.expressions.typed_expressions.ArrayNumericExpression[source]¶

Returns an array of integers from start to stop by step.

Examples

>>> hl.eval(hl.range(10))
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]

>>> hl.eval(hl.range(3, 10))
[3, 4, 5, 6, 7, 8, 9]

>>> hl.eval(hl.range(0, 10, step=3))
[0, 3, 6, 9]

Notes

The range includes start, but excludes stop.

If provided exactly one argument, the argument is interpreted as stop and start is set to zero. This matches the behavior of Python’s range.

Parameters:	start (int or `Expression` of type `tint32`) – Start of range. stop (int or `Expression` of type `tint32`) – End of range. step (int or `Expression` of type `tint32`) – Step of range.
Returns:	`ArrayInt32Expression`

class hail.expr.builders.CaseBuilder(missing_false=False)[source]¶

Class for chaining multiple if-else statements.

Examples

>>> x = hl.literal('foo bar baz')
>>> expr = (hl.case()
...           .when(x[:3] == 'FOO', 1)
...           .when(x.length() == 11, 2)
...           .when(x == 'secret phrase', 3)
...           .default(0))
>>> hl.eval(expr)
2

Notes

All expressions appearing as the then parameters to when() or default() method calls must be the same type.

Parameters:	missing_false (`bool`) – Treat missing predicates as `False`.

See also

case(), cond(), switch()

default(then)[source]¶

Finish the case statement by adding a default case.

Notes

If no condition from a when() call is True, then then is returned.

Parameters:	then (`Expression`)
Returns:	`Expression`

or_error(message)[source]¶

Finish the case statement by throwing an error with the given message.

Notes

If no condition from a CaseBuilder.when() call is True, then an error is thrown.

Parameters:	message (`Expression` of type `tstr`)
Returns:	`Expression`

or_missing()[source]¶

Finish the case statement by returning missing.

Notes

If no condition from a CaseBuilder.when() call is True, then the result is missing.

Parameters:	then (`Expression`)
Returns:	`Expression`

when(condition, then) → CaseBuilder[source]¶

Add a branch. If condition is True, then returns then.

Warning

Missingness is treated similarly to cond(). Missingness is not treated as False. A condition that evaluates to missing will return a missing result, not proceed to the next case. Always test missingness first in a CaseBuilder.

Parameters:	condition (`BooleanExpression`) then (`Expression`)
Returns:	`CaseBuilder` – Mutates and returns self.

class hail.expr.builders.SwitchBuilder(base)[source]¶

Class for generating conditional trees based on value of an expression.

Examples

>>> csq = hl.literal('loss of function')
>>> expr = (hl.switch(csq)
...           .when('synonymous', 1)
...           .when('SYN', 1)
...           .when('missense', 2)
...           .when('MIS', 2)
...           .when('loss of function', 3)
...           .when('LOF', 3)
...           .or_missing())
>>> hl.eval(expr)
3

Notes

All expressions appearing as the then parameters to when() or default() method calls must be the same type.

See also

case(), cond(), switch()

Parameters:	expr (`Expression`) – Value to match against.

default(then)[source]¶

Finish the switch statement by adding a default case.

Notes

If no value from a when() call is matched, then then is returned.

Parameters:	then (`Expression`)
Returns:	`Expression`

or_missing()[source]¶

Finish the switch statement by returning missing.

Notes

If no value from a when() call is matched, then the result is missing.

Parameters:	then (`Expression`)
Returns:	`Expression`

when(value, then) → SwitchBuilder[source]¶

Add a value test. If the base expression is equal to value, then: returns then.

Warning

Missingness always compares to missing. Both NA == NA and NA != NA return NA. Use when_missing() to test missingness.

Parameters:	value (`Expression`) then (`Expression`)
Returns:	`SwitchBuilder` – Mutates and returns self.

when_missing(then) → SwitchBuilder[source]¶

Add a test for missingness. If the base expression is missing, returns then.

Parameters:	then (`Expression`)
Returns:	`SwitchBuilder` – Mutates and returns self.