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 gff3leftjoin(table, features, seqid='seqid', start='start', end='end', proximity=1):
"""
Left join with a table of GFF3 features. See also :func:`petlx.interval.intervalleftjoin`.
.. versionadded:: 0.2
"""
return intervalleftjoin(table, features, lstart=start, lstop=end, lfacet=seqid,
rstart='start', rstop='end', rfacet='seqid',
proximity=proximity)
def test_intervalleftjoin_faceted_rkeymissing():
left = (('fruit', 'begin', 'end'),
('apple', 1, 2),
('orange', 5, 5))
right = (('type', 'start', 'stop', 'value'),
('apple', 1, 4, 'foo'))
expect = (('fruit', 'begin', 'end', 'type', 'start', 'stop', 'value'),
('apple', 1, 2, 'apple', 1, 4, 'foo'),
('orange', 5, 5, None, None, None, None))
actual = intervalleftjoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop', lfacet='fruit',
rfacet='type')
ieq(expect, actual)
ieq(expect, actual)
def test_intervalleftjoin_faceted_rkeymissing():
left = (('fruit', 'begin', 'end'),
('apple', 1, 2),
('orange', 5, 5))
right = (('type', 'start', 'stop', 'value'),
('apple', 1, 4, 'foo'))
expect = (('fruit', 'begin', 'end', 'type', 'start', 'stop', 'value'),
('apple', 1, 2, 'apple', 1, 4, 'foo'),
('orange', 5, 5, None, None, None, None))
actual = intervalleftjoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop', lfacet='fruit',
rfacet='type')
ieq(expect, actual)
ieq(expect, actual)
def test_intervalleftjoin_prefixes():
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 = intervalleftjoin(left, right,
lstart='begin', lstop='end',
rstart='start', rstop='stop',
lprefix='l_', rprefix='r_')
expect = (('l_begin', 'l_end', 'l_quux', 'r_start', 'r_stop', 'r_value'),
(1, 2, 'a', 1, 4, 'foo'),
(2, 4, 'b', 1, 4, 'foo'),
(2, 4, 'b', 3, 7, 'bar'),
(2, 5, 'c', 1, 4, 'foo'),
(2, 5, 'c', 3, 7, 'bar'),
(2, 5, 'c', 4, 9, 'baz'),
(9, 14, 'd', None, None, None),
(9, 140, 'e', None, None, None),
(1, 1, 'f', None, None, None),
(2, 2, 'g', 1, 4, 'foo'),
(4, 4, 'h', 3, 7, 'bar'),
(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_intervalleftjoin_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'),
('orange', 9, 14, None, None, None, None),
('orange', 19, 140, None, None, None, None),
('apple', 1, 1, None, None, None, None),
('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 = intervalleftjoin(left, right, lstart='begin', lstop='end',
rstart='start', rstop='stop', lfacet='fruit',
rfacet='type')
ieq(expect, actual)
ieq(expect, actual)
def test_intervalleftjoin_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'),
('orange', 9, 14, None, None, None, None),
('orange', 19, 140, None, None, None, None),
('apple', 1, 1, None, None, None, None),
('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 = intervalleftjoin(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 intervalleftjoin
look(left)
look(right)
result = intervalleftjoin(left, right, lstart='begin', lstop='end', rstart='start', rstop='stop')
look(result)
# fromhdf5
# set up a new hdf5 table to work with
import tables
h5file = tables.openFile("test1.h5", mode="w", title="Test file")
h5file.createGroup('/', 'testgroup', 'Test Group')
class FooBar(tables.IsDescription):
foo = tables.Int32Col(pos=0)
bar = tables.StringCol(6, pos=2)
h5table = h5file.createTable('/testgroup', 'testtable', FooBar, 'Test Table')
# load some data into the table
table1 = (('foo', 'bar'),
# intervalleftjoin
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 intervalleftjoin
look(left)
look(right)
result = intervalleftjoin(left,
right,
lstart='begin',
lstop='end',
rstart='start',
rstop='stop')
look(result)
# fromhdf5
# set up a new hdf5 table to work with
import tables
h5file = tables.openFile("test1.h5", mode="w", title="Test file")
h5file.createGroup('/', 'testgroup', 'Test Group')
class FooBar(tables.IsDescription):
foo = tables.Int32Col(pos=0)
bar = tables.StringCol(6, pos=2)
