Core language functions

eval(expression)

Evaluate a Hail expression, returning the result.

literal(x, dtype, str, None] = None)

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

cond(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.eval(expression)[source]

Evaluate a Hail expression, returning the result.

This method is extremely useful for learning about Hail expressions and understanding how to compose them.

The expression must have no indices, but can refer to the globals of a Table or MatrixTable.

Examples

Evaluate a conditional:

>>> x = 6
>>> hl.eval(hl.cond(x % 2 == 0, 'Even', 'Odd'))
'Even'
Parameters

expression (Expression) – Any expression, or a Python value that can be implicitly interpreted as an expression.

Returns

Any

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]

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()

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
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.

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

BooleanExpressionTrue 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

BooleanExpressionTrue 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
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
Returns

Expression – This expression has the same type as b.

hail.expr.functions.range(start, stop, 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(0, 10))
[0, 1, 2, 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.

Parameters
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
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
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.