def test_intervaljoins_faceted_compound():
left = (('fruit', 'sort', 'begin', 'end'),
('apple', 'cox', 1, 2),
('apple', 'fuji', 2, 4))
right = (('type', 'variety', 'start', 'stop', 'value'),
('apple', 'cox', 1, 4, 'foo'),
('apple', 'fuji', 3, 7, 'bar'),
('orange', 'mandarin', 4, 9, 'baz'))
expect = (('fruit', 'sort', 'begin', 'end', 'type', 'variety', 'start',
'stop', 'value'),
('apple', 'cox', 1, 2, 'apple', 'cox', 1, 4, 'foo'),
('apple', 'fuji', 2, 4, 'apple', 'fuji', 3, 7, 'bar'))
actual = intervaljoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop',
lfacet=('fruit', 'sort'),
rfacet=('type', 'variety'))
ieq(expect, actual)
ieq(expect, actual)
actual = intervalleftjoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop',
lfacet=('fruit', 'sort'),
rfacet=('type', 'variety'))
ieq(expect, actual)
ieq(expect, actual)
def gff3join(table, features, seqid='seqid', start='start', end='end', proximity=1):
"""
Join with a table of GFF3 features. See also :func:`petlx.interval.intervaljoin`.
.. versionadded:: 0.2
"""
return intervaljoin(table, features, lstart=start, lstop=end, lfacet=seqid,
rstart='start', rstop='end', rfacet='seqid',
proximity=proximity)
def test_intervaljoin_proximity():
left = (('begin', 'end', 'quux'),
(1, 2, 'a'),
(2, 4, 'b'),
(2, 5, 'c'),
(9, 14, 'd'),
(9, 140, 'e'),
(1, 1, 'f'),
(2, 2, 'g'),
(4, 4, 'h'),
(5, 5, 'i'),
(1, 8, 'j'))
right = (('start', 'stop', 'value'),
(1, 4, 'foo'),
(3, 7, 'bar'),
(4, 9, 'baz'))
actual = intervaljoin(left, right,
lstart='begin', lstop='end',
rstart='start', rstop='stop',
proximity=1)
expect = (('begin', 'end', 'quux', 'start', 'stop', 'value'),
(1, 2, 'a', 1, 4, 'foo'),
(2, 4, 'b', 1, 4, 'foo'),
(2, 4, 'b', 3, 7, 'bar'),
(2, 4, 'b', 4, 9, 'baz'),
(2, 5, 'c', 1, 4, 'foo'),
(2, 5, 'c', 3, 7, 'bar'),
(2, 5, 'c', 4, 9, 'baz'),
(9, 14, 'd', 4, 9, 'baz'),
(9, 140, 'e', 4, 9, 'baz'),
(1, 1, 'f', 1, 4, 'foo'),
(2, 2, 'g', 1, 4, 'foo'),
(4, 4, 'h', 1, 4, 'foo'),
(4, 4, 'h', 3, 7, 'bar'),
(4, 4, 'h', 4, 9, 'baz'),
(5, 5, 'i', 3, 7, 'bar'),
(5, 5, 'i', 4, 9, 'baz'),
(1, 8, 'j', 1, 4, 'foo'),
(1, 8, 'j', 3, 7, 'bar'),
(1, 8, 'j', 4, 9, 'baz'))
ieq(expect, actual)
ieq(expect, actual)
def test_intervaljoin_proximity():
left = (('begin', 'end', 'quux'),
(1, 2, 'a'),
(2, 4, 'b'),
(2, 5, 'c'),
(9, 14, 'd'),
(9, 140, 'e'),
(1, 1, 'f'),
(2, 2, 'g'),
(4, 4, 'h'),
(5, 5, 'i'),
(1, 8, 'j'))
right = (('start', 'stop', 'value'),
(1, 4, 'foo'),
(3, 7, 'bar'),
(4, 9, 'baz'))
actual = intervaljoin(left, right,
lstart='begin', lstop='end',
rstart='start', rstop='stop',
proximity=1)
expect = (('begin', 'end', 'quux', 'start', 'stop', 'value'),
(1, 2, 'a', 1, 4, 'foo'),
(2, 4, 'b', 1, 4, 'foo'),
(2, 4, 'b', 3, 7, 'bar'),
(2, 4, 'b', 4, 9, 'baz'),
(2, 5, 'c', 1, 4, 'foo'),
(2, 5, 'c', 3, 7, 'bar'),
(2, 5, 'c', 4, 9, 'baz'),
(9, 14, 'd', 4, 9, 'baz'),
(9, 140, 'e', 4, 9, 'baz'),
(1, 1, 'f', 1, 4, 'foo'),
(2, 2, 'g', 1, 4, 'foo'),
(4, 4, 'h', 1, 4, 'foo'),
(4, 4, 'h', 3, 7, 'bar'),
(4, 4, 'h', 4, 9, 'baz'),
(5, 5, 'i', 3, 7, 'bar'),
(5, 5, 'i', 4, 9, 'baz'),
(1, 8, 'j', 1, 4, 'foo'),
(1, 8, 'j', 3, 7, 'bar'),
(1, 8, 'j', 4, 9, 'baz'))
ieq(expect, actual)
ieq(expect, actual)
def test_intervaljoin_faceted():
left = (('fruit', 'begin', 'end'),
('apple', 1, 2),
('apple', 2, 4),
('apple', 2, 5),
('orange', 2, 5),
('orange', 9, 14),
('orange', 19, 140),
('apple', 1, 1),
('apple', 2, 2),
('apple', 4, 4),
('apple', 5, 5),
('orange', 5, 5))
right = (('type', 'start', 'stop', 'value'),
('apple', 1, 4, 'foo'),
('apple', 3, 7, 'bar'),
('orange', 4, 9, 'baz'))
expect = (('fruit', 'begin', 'end', 'type', 'start', 'stop', 'value'),
('apple', 1, 2, 'apple', 1, 4, 'foo'),
('apple', 2, 4, 'apple', 1, 4, 'foo'),
('apple', 2, 4, 'apple', 3, 7, 'bar'),
('apple', 2, 5, 'apple', 1, 4, 'foo'),
('apple', 2, 5, 'apple', 3, 7, 'bar'),
('orange', 2, 5, 'orange', 4, 9, 'baz'),
('apple', 2, 2, 'apple', 1, 4, 'foo'),
('apple', 4, 4, 'apple', 3, 7, 'bar'),
('apple', 5, 5, 'apple', 3, 7, 'bar'),
('orange', 5, 5, 'orange', 4, 9, 'baz'))
actual = intervaljoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop', lfacet='fruit',
rfacet='type')
ieq(expect, actual)
ieq(expect, actual)
def test_intervaljoin_faceted():
left = (('fruit', 'begin', 'end'),
('apple', 1, 2),
('apple', 2, 4),
('apple', 2, 5),
('orange', 2, 5),
('orange', 9, 14),
('orange', 19, 140),
('apple', 1, 1),
('apple', 2, 2),
('apple', 4, 4),
('apple', 5, 5),
('orange', 5, 5))
right = (('type', 'start', 'stop', 'value'),
('apple', 1, 4, 'foo'),
('apple', 3, 7, 'bar'),
('orange', 4, 9, 'baz'))
expect = (('fruit', 'begin', 'end', 'type', 'start', 'stop', 'value'),
('apple', 1, 2, 'apple', 1, 4, 'foo'),
('apple', 2, 4, 'apple', 1, 4, 'foo'),
('apple', 2, 4, 'apple', 3, 7, 'bar'),
('apple', 2, 5, 'apple', 1, 4, 'foo'),
('apple', 2, 5, 'apple', 3, 7, 'bar'),
('orange', 2, 5, 'orange', 4, 9, 'baz'),
('apple', 2, 2, 'apple', 1, 4, 'foo'),
('apple', 4, 4, 'apple', 3, 7, 'bar'),
('apple', 5, 5, 'apple', 3, 7, 'bar'),
('orange', 5, 5, 'orange', 4, 9, 'baz'))
actual = intervaljoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop', lfacet='fruit',
rfacet='type')
ieq(expect, actual)
ieq(expect, actual)
(9, 140, 'e'),
(1, 1, 'f'),
(2, 2, 'g'),
(4, 4, 'h'),
(5, 5, 'i'),
(1, 8, 'j'))
right = (('start', 'stop', 'value'),
(1, 4, 'foo'),
(3, 7, 'bar'),
(4, 9, 'baz'))
from petl import look
from petlx.interval import intervaljoin
look(left)
look(right)
result = intervaljoin(left, right, lstart='begin', lstop='end', rstart='start', rstop='stop')
look(result)
# intervaljoin with facet
left = (('fruit', 'begin', 'end'),
('apple', 1, 2),
('apple', 2, 4),
('apple', 2, 5),
('orange', 2, 5),
('orange', 9, 14),
('orange', 19, 140),
('apple', 1, 1),
('apple', 2, 2),
('apple', 4, 4),
lkp['orange'][8]
# intervaljoin
left = (('begin', 'end', 'quux'), (1, 2, 'a'), (2, 4, 'b'), (2, 5, 'c'),
(9, 14, 'd'), (9, 140, 'e'), (1, 1, 'f'), (2, 2, 'g'), (4, 4, 'h'),
(5, 5, 'i'), (1, 8, 'j'))
right = (('start', 'stop', 'value'), (1, 4, 'foo'), (3, 7, 'bar'), (4, 9,
'baz'))
from petl import look
from petlx.interval import intervaljoin
look(left)
look(right)
result = intervaljoin(left,
right,
lstart='begin',
lstop='end',
rstart='start',
rstop='stop')
look(result)
# intervaljoin with facet
left = (('fruit', 'begin', 'end'), ('apple', 1, 2), ('apple', 2, 4),
('apple', 2, 5), ('orange', 2, 5), ('orange', 9, 14),
('orange', 19, 140), ('apple', 1, 1), ('apple', 2, 2), ('apple', 4, 4),
('apple', 5, 5), ('orange', 5, 5))
right = (('type', 'start', 'stop', 'value'), ('apple', 1, 4, 'foo'),
('apple', 3, 7, 'bar'), ('orange', 4, 9, 'baz'))
from petl import look
from petlx.interval import intervaljoin