Interval¶
-
class
hail.representation.
Interval
(start, end)[source]¶ A genomic interval marked by start and end loci.
Parameters: Attributes
end
Locus object referring to the end of the interval (exclusive). start
Locus object referring to the start of the interval (inclusive). Methods
__init__
contains
True if the supplied locus is contained within the interval. overlaps
True if the the supplied interval contains any locus in common with this one. parse
Parses a genomic interval from string representation. -
contains
(locus)[source]¶ True if the supplied locus is contained within the interval.
This membership check is left-inclusive, right-exclusive. This means that the interval 1:100-101 includes 1:100 but not 1:101.
Type: locus: Locus.
Return type: bool
-
overlaps
(interval)[source]¶ True if the the supplied interval contains any locus in common with this one.
The statement
>>> interval1.overlaps(interval2)
is equivalent to
>>> interval1.contains(interval2.start) or interval2.contains(interval1.start)
Type: interval: Interval
Return type: bool
-
static
parse
(string)[source]¶ Parses a genomic interval from string representation.
Examples:
>>> interval_1 = Interval.parse('X:100005-X:150020') >>> interval_2 = Interval.parse('16:29500000-30200000') >>> interval_3 = Interval.parse('16:29.5M-30.2M') # same as interval_2 >>> interval_4 = Interval.parse('16:30000000-END') >>> interval_5 = Interval.parse('16:30M-END') # same as interval_4 >>> interval_6 = Interval.parse('1-22') # autosomes >>> interval_7 = Interval.parse('X') # all of chromosome X
There are several acceptable representations.
CHR1:POS1-CHR2:POS2
is the fully specified representation, and we use this to define the various shortcut representations.In a
POS
field,start
(Start
,START
) stands for 0.In a
POS
field,end
(End
,END
) stands for max int.In a
POS
field, the qualifiersm
(M
) andk
(K
) multiply the given number by1,000,000
and1,000
, respectively.1.6K
is short for 1600, and29M
is short for 29000000.CHR:POS1-POS2
stands forCHR:POS1-CHR:POS2
CHR1-CHR2
stands forCHR1:START-CHR2:END
CHR
stands forCHR:START-CHR:END
Note that the start locus must precede the start locus.
Return type: Interval
-