BooleanExpression

class hail.expr.BooleanExpression[source]

Bases: hail.expr.expressions.typed_expressions.NumericExpression

Expression of type tbool.

>>> t = hl.literal(True)
>>> f = hl.literal(False)
>>> na = hl.null(hl.tbool)
>>> hl.eval(t)
True
>>> hl.eval(f)
False
>>> hl.eval(na)
None

Attributes

dtype

The data type of the expression.

Methods

__add__(other)

Add two numbers.

Examples

>>> hl.eval(x + 2)
5
>>> hl.eval(x + y)
7.5
Parameters

other (NumericExpression) – Number to add.

Returns

NumericExpression – Sum of the two numbers.

__and__(other)[source]

Return True if the left and right arguments are True.

Examples

>>> hl.eval(t & f)
False
>>> hl.eval(t & na)
None
>>> hl.eval(f & na)
False

The & and | operators have higher priority than comparison operators like ==, <, or >. Parentheses are often necessary:

>>> x = hl.literal(5)
>>> hl.eval((x < 10) & (x > 2))
True
Parameters

other (BooleanExpression) – Right-side operand.

Returns

BooleanExpressionTrue if both left and right are True.

__eq__(other)

Returns True if the two expressions are equal.

Examples

>>> x = hl.literal(5)
>>> y = hl.literal(5)
>>> z = hl.literal(1)
>>> hl.eval(x == y)
True
>>> hl.eval(x == z)
False

Notes

This method will fail with an error if the two expressions are not of comparable types.

Parameters

other (Expression) – Expression for equality comparison.

Returns

BooleanExpressionTrue if the two expressions are equal.

__floordiv__(other)

Divide two numbers with floor division.

Examples

>>> hl.eval(x // 2)
1
>>> hl.eval(y // 2)
2.0
Parameters

other (NumericExpression) – Dividend.

Returns

NumericExpression – The floor of the left number divided by the right.

__ge__(other)

Greater-than-or-equals comparison.

Examples

>>> hl.eval(y >= 4)
True
Parameters

other (NumericExpression) – Right side for comparison.

Returns

BooleanExpressionTrue if the left side is greater than or equal to the right side.

__gt__(other)

Greater-than comparison.

Examples

>>> hl.eval(y > 4)
True
Parameters

other (NumericExpression) – Right side for comparison.

Returns

BooleanExpressionTrue if the left side is greater than the right side.

__invert__()[source]

Return the boolean negation.

Examples

>>> hl.eval(~t)
False
>>> hl.eval(~f)
True
>>> hl.eval(~na)
None
Returns

BooleanExpression – Boolean negation.

__le__(other)

Less-than-or-equals comparison.

Examples

>>> hl.eval(x <= 3)
True
Parameters

other (NumericExpression) – Right side for comparison.

Returns

BooleanExpressionTrue if the left side is smaller than or equal to the right side.

__lt__(other)

Less-than comparison.

Examples

>>> hl.eval(x < 5)
True
Parameters

other (NumericExpression) – Right side for comparison.

Returns

BooleanExpressionTrue if the left side is smaller than the right side.

__mod__(other)

Compute the left modulo the right number.

Examples

>>> hl.eval(32 % x)
2
>>> hl.eval(7 % y)
2.5
Parameters

other (NumericExpression) – Dividend.

Returns

NumericExpression – Remainder after dividing the left by the right.

__mul__(other)

Multiply two numbers.

Examples

>>> hl.eval(x * 2)
6
>>> hl.eval(x * y)
13.5
Parameters

other (NumericExpression) – Number to multiply.

Returns

NumericExpression – Product of the two numbers.

__ne__(other)

Returns True if the two expressions are not equal.

Examples

>>> x = hl.literal(5)
>>> y = hl.literal(5)
>>> z = hl.literal(1)
>>> hl.eval(x != y)
False
>>> hl.eval(x != z)
True

Notes

This method will fail with an error if the two expressions are not of comparable types.

Parameters

other (Expression) – Expression for inequality comparison.

Returns

BooleanExpressionTrue if the two expressions are not equal.

__neg__()

Negate the number (multiply by -1).

Examples

>>> hl.eval(-x)
-3
Returns

NumericExpression – Negated number.

__or__(other)[source]

Return True if at least one of the left and right arguments is True.

Examples

>>> hl.eval(t | f)
True
>>> hl.eval(t | na)
True
>>> hl.eval(f | na)
None

The & and | operators have higher priority than comparison operators like ==, <, or >. Parentheses are often necessary:

>>> x = hl.literal(5)
>>> hl.eval((x < 10) | (x > 20))
True
Parameters

other (BooleanExpression) – Right-side operand.

Returns

BooleanExpressionTrue if either left or right is True.

__pow__(power, modulo=None)

Raise the left to the right power.

Examples

>>> hl.eval(x ** 2)
9.0
>>> hl.eval(x ** -2)
0.1111111111111111
>>> hl.eval(y ** 1.5)
9.545941546018392
Parameters
Returns

Expression of type tfloat64 – Result of raising left to the right power.

__sub__(other)

Subtract the right number from the left.

Examples

>>> hl.eval(x - 2)
1
>>> hl.eval(x - y)
-1.5
Parameters

other (NumericExpression) – Number to subtract.

Returns

NumericExpression – Difference of the two numbers.

__truediv__(other)

Divide two numbers.

Examples

>>> hl.eval(x / 2)
1.5
>>> hl.eval(y / 0.1)
45.0
Parameters

other (NumericExpression) – Dividend.

Returns

NumericExpression – The left number divided by the left.

collect(_localize=True)

Collect all records of an expression into a local list.

Examples

Collect all the values from C1:

>>> table1.C1.collect()
[2, 2, 10, 11]

Warning

Extremely experimental.

Warning

The list of records may be very large.

Returns

list

describe(handler=<built-in function print>)

Print information about type, index, and dependencies.

property dtype

The data type of the expression.

Returns

HailType

export(path, delimiter='\t', missing='NA', header=True)

Export a field to a text file.

Examples

>>> small_mt.GT.export('output/gt.tsv')
>>> with open('output/gt.tsv', 'r') as f:
...     for line in f:
...         print(line, end='')
locus   alleles 0       1       2       3
1:1     ["A","C"]       0/1     0/1     0/0     0/0
1:2     ["A","C"]       1/1     0/1     1/1     1/1
1:3     ["A","C"]       1/1     0/1     0/1     0/0
1:4     ["A","C"]       1/1     0/1     1/1     1/1
>>> small_mt.GT.export('output/gt-no-header.tsv', header=False)
>>> with open('output/gt-no-header.tsv', 'r') as f:
...     for line in f:
...         print(line, end='')
1:1     ["A","C"]       0/1     0/1     0/0     0/0
1:2     ["A","C"]       1/1     0/1     1/1     1/1
1:3     ["A","C"]       1/1     0/1     0/1     0/0
1:4     ["A","C"]       1/1     0/1     1/1     1/1
>>> small_mt.pop.export('output/pops.tsv')
>>> with open('output/pops.tsv', 'r') as f:
...     for line in f:
...         print(line, end='')
sample_idx      pop
0       2
1       2
2       0
3       2
>>> small_mt.ancestral_af.export('output/ancestral_af.tsv')
>>> with open('output/ancestral_af.tsv', 'r') as f:
...     for line in f:
...         print(line, end='')
locus   alleles ancestral_af
1:1     ["A","C"]       5.3905e-01
1:2     ["A","C"]       8.6768e-01
1:3     ["A","C"]       4.3765e-01
1:4     ["A","C"]       7.6300e-01
>>> mt = small_mt
>>> small_mt.bn.export('output/bn.tsv')
>>> with open('output/bn.tsv', 'r') as f:
...     for line in f:
...         print(line, end='')
bn
{"n_populations":3,"n_samples":4,"n_variants":4,"n_partitions":8,"pop_dist":[1,1,1],"fst":[0.1,0.1,0.1],"mixture":false}

Notes

For entry-indexed expressions, if there is one column key field, the result of calling hl.str() on that field is used as the column header. Otherwise, each compound column key is converted to JSON and used as a column header. For example:

>>> small_mt = small_mt.key_cols_by(s=small_mt.sample_idx, family='fam1')
>>> small_mt.GT.export('output/gt-no-header.tsv')
>>> with open('output/gt-no-header.tsv', 'r') as f:
...     for line in f:
...         print(line, end='')
locus   alleles {"s":0,"family":"fam1"} {"s":1,"family":"fam1"} {"s":2,"family":"fam1"} {"s":3,"family":"fam1"}
1:1     ["A","C"]       0/1     0/1     0/0     0/0
1:2     ["A","C"]       1/1     0/1     1/1     1/1
1:3     ["A","C"]       1/1     0/1     0/1     0/0
1:4     ["A","C"]       1/1     0/1     1/1     1/1
Parameters
  • path (str) – The path to which to export.

  • delimiter (str) – The string for delimiting columns.

  • missing (str) – The string to output for missing values.

  • header (bool) – When True include a header line.

show(n=None, width=None, truncate=None, types=True, handler=None, n_rows=None, n_cols=None)

Print the first few rows of the table to the console.

Examples

>>> table1.SEX.show()
+-------+-----+
|    ID | SEX |
+-------+-----+
| int32 | str |
+-------+-----+
|     1 | "M" |
|     2 | "M" |
|     3 | "F" |
|     4 | "F" |
+-------+-----+
>>> hl.literal(123).show()
+--------+
| <expr> |
+--------+
|  int32 |
+--------+
|    123 |
+--------+

Warning

Extremely experimental.

Parameters
  • n (int) – Maximum number of rows to show.

  • width (int) – Horizontal width at which to break columns.

  • truncate (int, optional) – Truncate each field to the given number of characters. If None, truncate fields to the given width.

  • types (bool) – Print an extra header line with the type of each field.

summarize(handler=None)

Compute and print summary information about the expression.

Danger

This functionality is experimental. It may not be tested as well as other parts of Hail and the interface is subject to change.

take(n, _localize=True)

Collect the first n records of an expression.

Examples

Take the first three rows:

>>> table1.X.take(3)
[5, 6, 7]

Warning

Extremely experimental.

Parameters

n (int) – Number of records to take.

Returns

list