CallExpression

class hail.expr.CallExpression[source]

Expression of type tcall.

>>> call = hl.call(0, 1, phased=False)

Attributes

dtype

The data type of the expression.

phased

True if the call is phased.

ploidy

Return the number of alleles of this call.

Methods

is_diploid

True if the call has ploidy equal to 2.

is_haploid

True if the call has ploidy equal to 1.

is_het

Evaluate whether the call includes two different alleles.

is_het_non_ref

Evaluate whether the call includes two different alleles, neither of which is reference.

is_het_ref

Evaluate whether the call includes two different alleles, one of which is reference.

is_hom_ref

Evaluate whether the call includes two reference alleles.

is_hom_var

Evaluate whether the call includes two identical alternate alleles.

is_non_ref

Evaluate whether the call includes one or more non-reference alleles.

n_alt_alleles

Returns the number of non-reference alleles.

one_hot_alleles

Returns an array containing the summed one-hot encoding of the alleles.

unphased_diploid_gt_index

Return the genotype index for unphased, diploid calls.

__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.

__ge__(other)

Return self>=value.

__getitem__(item)[source]

Get the i*th* allele.

Examples

Index with a single integer:

>>> hl.eval(call[0])
0
>>> hl.eval(call[1])
1
Parameters

item (int or Expression of type tint32) – Allele index.

Returns

Expression of type tint32

__gt__(other)

Return self>value.

__le__(other)

Return self<=value.

__lt__(other)

Return self<value.

__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.

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 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.

is_diploid()[source]

True if the call has ploidy equal to 2.

Examples

>>> hl.eval(call.is_diploid())
True
Returns

BooleanExpression

is_haploid()[source]

True if the call has ploidy equal to 1.

Examples

>>> hl.eval(call.is_haploid())
False
Returns

BooleanExpression

is_het()[source]

Evaluate whether the call includes two different alleles.

Examples

>>> hl.eval(call.is_het())
True

Notes

In the diploid biallelic case, a 0/1 call will return True, and 0/0 and 1/1 will return False.

Returns

BooleanExpressionTrue if the two alleles are different, False if they are the same.

is_het_non_ref()[source]

Evaluate whether the call includes two different alleles, neither of which is reference.

Examples

>>> hl.eval(call.is_het_non_ref())
False

Notes

A biallelic variant may never have a het-non-ref call. Examples of these calls are 1/2 and 2/4.

Returns

BooleanExpressionTrue if the call includes two different alternate alleles, False otherwise.

is_het_ref()[source]

Evaluate whether the call includes two different alleles, one of which is reference.

Examples

>>> hl.eval(call.is_het_ref())
True
Returns

BooleanExpressionTrue if the call includes one reference and one alternate allele, False otherwise.

is_hom_ref()[source]

Evaluate whether the call includes two reference alleles.

Examples

>>> hl.eval(call.is_hom_ref())
False
Returns

BooleanExpressionTrue if the call includes two reference alleles, False otherwise.

is_hom_var()[source]

Evaluate whether the call includes two identical alternate alleles.

Examples

>>> hl.eval(call.is_hom_var())
False
Returns

BooleanExpressionTrue if the call includes two identical alternate alleles, False otherwise.

is_non_ref()[source]

Evaluate whether the call includes one or more non-reference alleles.

Examples

>>> hl.eval(call.is_non_ref())
True

Notes

In the diploid biallelic case, a 0/0 call will return False, and 0/1 and 1/1 will return True.

Returns

BooleanExpressionTrue if at least one allele is non-reference, False otherwise.

n_alt_alleles()[source]

Returns the number of non-reference alleles.

Examples

>>> hl.eval(call.n_alt_alleles())
1

Notes

For diploid biallelic calls, this method is equivalent to the alternate allele dosage. For instance, 0/0 will return 0, 0/1 will return 1, and 1/1 will return 2.

Returns

Expression of type tint32 – The number of non-reference alleles.

one_hot_alleles(alleles)[source]

Returns an array containing the summed one-hot encoding of the alleles.

Examples

Compute one-hot encoding when number of total alleles is 2.

>>> hl.eval(call.one_hot_alleles(2))
[1, 1]

DEPRECATED: Compute one-hot encoding based on length of list of alleles.

>>> hl.eval(call.one_hot_alleles(['A', 'T']))
[1, 1]

This one-hot representation is the positional sum of the one-hot encoding for each called allele. For a biallelic variant, the one-hot encoding for a reference allele is [1, 0] and the one-hot encoding for an alternate allele is [0, 1]. Diploid calls would produce the following arrays: [2, 0] for homozygous reference, [1, 1] for heterozygous, and [0, 2] for homozygous alternate.

Parameters

alleles (Int32Expression or ArrayExpression of tstr.) – Number of total alleles, including the reference, or array of variant alleles.

Returns

ArrayExpression of tint32 – An array of summed one-hot encodings of allele indices.

property phased

True if the call is phased.

Examples

>>> hl.eval(call.phased)
False
Returns

BooleanExpression

property ploidy

Return the number of alleles of this call.

Examples

>>> hl.eval(call.ploidy)
2

Notes

Currently only ploidy 1 and 2 are supported.

Returns

Expression of type tint32

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

Print the first few records of the expression to the console.

If the expression refers to a value on a keyed axis of a table or matrix table, then the accompanying keys will be shown along with the records.

Examples

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

Notes

The output can be passed piped to another output source using the handler argument:

>>> ht.foo.show(handler=lambda x: logging.info(x))  
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

unphased_diploid_gt_index()[source]

Return the genotype index for unphased, diploid calls.

Examples

>>> hl.eval(call.unphased_diploid_gt_index())
1
Returns

Expression of type tint32