IntervalExpression
- class hail.expr.IntervalExpression[source]
Expression of type
tinterval.>>> interval = hl.interval(3, 11) >>> locus_interval = hl.parse_locus_interval("1:53242-90543")
Attributes
The data type of the expression.
Returns the end point.
True if the interval includes the end point.
True if the interval includes the start point.
Returns the start point.
Methods
Tests whether a value is contained in the interval.
True if the the supplied interval contains any value in common with this one.
- __eq__(other)
Returns
Trueif 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:
BooleanExpression–Trueif the two expressions are equal.
- __ge__(other)
Return self>=value.
- __gt__(other)
Return self>value.
- __le__(other)
Return self<=value.
- __lt__(other)
Return self<value.
- __ne__(other)
Returns
Trueif 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:
BooleanExpression–Trueif 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:
- contains(value)[source]
Tests whether a value is contained in the interval.
Examples
>>> hl.eval(interval.contains(3)) True
>>> hl.eval(interval.contains(11)) False
- Parameters:
value – Object with type matching the interval point type.
- Returns:
BooleanExpression–Trueif value is contained in the interval,Falseotherwise.
- describe(handler=<built-in function print>)
Print information about type, index, and dependencies.
- property end
Returns the end point.
Examples
>>> hl.eval(interval.end) 11
- Returns:
- 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 0/0 0/1 0/0 1:2 ["A","C"] 1/1 0/1 0/1 0/1 1:3 ["A","C"] 0/0 0/1 0/0 0/0 1:4 ["A","C"] 0/1 1/1 0/1 0/1
>>> 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 0/0 0/1 0/0 1:2 ["A","C"] 1/1 0/1 0/1 0/1 1:3 ["A","C"] 0/0 0/1 0/0 0/0 1:4 ["A","C"] 0/1 1/1 0/1 0/1
>>> 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 1 1 2 2 2 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"] 3.8152e-01 1:2 ["A","C"] 7.0588e-01 1:3 ["A","C"] 4.9991e-01 1:4 ["A","C"] 3.9616e-01
>>> 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":4,"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 0/0 0/1 0/0 1:2 ["A","C"] 1/1 0/1 0/1 0/1 1:3 ["A","C"] 0/0 0/1 0/0 0/0 1:4 ["A","C"] 0/1 1/1 0/1 0/1
- property includes_end
True if the interval includes the end point.
Examples
>>> hl.eval(interval.includes_end) False
- Returns:
- property includes_start
True if the interval includes the start point.
Examples
>>> hl.eval(interval.includes_start) True
- Returns:
- overlaps(interval)[source]
True if the the supplied interval contains any value in common with this one.
Examples
>>> hl.eval(interval.overlaps(hl.interval(5, 9))) True
>>> hl.eval(interval.overlaps(hl.interval(11, 20))) False
- Parameters:
interval (
Expressionwith typetinterval) – Interval object with the same point type.- Returns:
- 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:
- property start
Returns the start point.
Examples
>>> hl.eval(interval.start) 3
- Returns:
- 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.