Expression

class hail.expr.Expression[source]

Bases: object

Base class for Hail expressions.

Attributes

dtype The data type of the expression.

Methods

__init__ Initialize self.
collect Collect all records of an expression into a local list.
describe Print information about type, index, and dependencies.
export Export a field to a text file.
show Print the first few rows of the table to the console.
summarize Compute and print summary information about the expression.
take Collect the first n records of an expression.
__eq__(other)[source]

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.
__ge__(other)[source]

Return self>=value.

__gt__(other)[source]

Return self>value.

__le__(other)[source]

Return self<=value.

__lt__(other)[source]

Return self<value.

__ne__(other)[source]

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.
collect(_localize=True)[source]

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>)[source]

Print information about type, index, and dependencies.

dtype

The data type of the expression.

Returns:HailType
export(path, delimiter='\t', missing='NA', header=True)[source]

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)[source]

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)[source]

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)[source]

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