def test_teehtml():
t1 = (('foo', 'bar'), ('a', 2), ('b', 1), ('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teehtml(f1.name).selectgt('bar', 1).topickle(f2.name)
ieq(t1, etl.fromxml(f1.name, './/tr', ('th', 'td')).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_teepickle():
t1 = (('foo', 'bar'), ('a', 2), ('b', 1), ('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teepickle(f1.name).selectgt('bar', 1).topickle(f2.name)
ieq(t1, etl.frompickle(f1.name))
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_container():
table = (('foo', 'bar'), ('a', 1), ('b', 2), ('c', 2))
actual = etl.wrap(table)[0]
expect = ('foo', 'bar')
eq_(expect, actual)
actual = etl.wrap(table)['bar']
expect = (1, 2, 2)
ieq(expect, actual)
actual = len(etl.wrap(table))
expect = 4
eq_(expect, actual)
def test_teetsv():
t1 = (('foo', 'bar'), ('a', 2), ('b', 1), ('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teetsv(f1.name).selectgt('bar', 1).totsv(f2.name)
ieq(t1, etl.fromtsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.fromtsv(f2.name).convertnumbers())
def test_teeuhtml():
t1 = ((u'foo', u'bar'), (u'Արամ Խաչատրյան', 2), (u'Johann Strauß', 1),
(u'Вагиф Сәмәдоғлу', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teeuhtml(f1.name).selectgt('bar', 1).topickle(f2.name)
ieq(t1, etl.fromxml(f1.name, './/tr', ('th', 'td')).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_teepickle():
t1 = (('foo', 'bar'),
('a', 2),
('b', 1),
('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teepickle(f1.name).selectgt('bar', 1).topickle(f2.name)
ieq(t1, etl.frompickle(f1.name))
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_teeuhtml():
t1 = ((u'foo', u'bar'),
(u'Արամ Խաչատրյան', 2),
(u'Johann Strauß', 1),
(u'Вагиф Сәмәдоғлу', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teeuhtml(f1.name).selectgt('bar', 1).topickle(f2.name)
ieq(t1, etl.fromxml(f1.name, './/tr', ('th', 'td')).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_teehtml():
t1 = (('foo', 'bar'),
('a', 2),
('b', 1),
('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teehtml(f1.name).selectgt('bar', 1).topickle(f2.name)
ieq(t1, etl.fromxml(f1.name, './/tr', ('th', 'td')).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_container():
table = (('foo', 'bar'),
('a', 1),
('b', 2),
('c', 2))
actual = etl.wrap(table)[0]
expect = ('foo', 'bar')
eq_(expect, actual)
actual = etl.wrap(table)['bar']
expect = (1, 2, 2)
ieq(expect, actual)
actual = len(etl.wrap(table))
expect = 4
eq_(expect, actual)
def test_teetext():
t1 = (('foo', 'bar'),
('a', 2),
('b', 1),
('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
prologue = 'foo,bar\n'
template = '{foo},{bar}\n'
epilogue = 'd,4'
(etl
.wrap(t1)
.teetext(f1.name,
template=template,
prologue=prologue,
epilogue=epilogue)
.selectgt('bar', 1)
.topickle(f2.name))
ieq(t1 + (('d', 4),),
etl.fromcsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1),
etl.frompickle(f2.name))
def test_values_container_convenience_methods():
table = etl.wrap((('foo', 'bar'),
('a', 1),
('b', 2),
('c', 2)))
actual = table.values('foo').set()
expect = set(['a', 'b', 'c'])
eq_(expect, actual)
actual = table.values('foo').list()
expect = ['a', 'b', 'c']
eq_(expect, actual)
actual = table.values('foo').tuple()
expect = ('a', 'b', 'c')
eq_(expect, actual)
actual = table.values('bar').sum()
expect = 5
eq_(expect, actual)
actual = table.data().dict()
expect = {'a': 1, 'b': 2, 'c': 2}
eq_(expect, actual)
def test_teeutext():
t1 = ((u'foo', u'bar'),
(u'Արամ Խաչատրյան', 2),
(u'Johann Strauß', 1),
(u'Вагиф Сәмәдоғлу', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
prologue = u'foo,bar\n'
template = u'{foo},{bar}\n'
epilogue = u'章子怡,4'
(etl
.wrap(t1)
.teeutext(f1.name,
template=template,
prologue=prologue,
epilogue=epilogue)
.selectgt('bar', 1)
.topickle(f2.name))
ieq(t1 + ((u'章子怡', 4),),
etl.fromucsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1),
etl.frompickle(f2.name))
def test_values_container_convenience_methods():
table = etl.wrap((('foo', 'bar'),
('a', 1),
('b', 2),
('c', 2)))
actual = table.values('foo').set()
expect = set(['a', 'b', 'c'])
eq_(expect, actual)
actual = table.values('foo').list()
expect = ['a', 'b', 'c']
eq_(expect, actual)
actual = table.values('foo').tuple()
expect = ('a', 'b', 'c')
eq_(expect, actual)
actual = table.values('bar').sum()
expect = 5
eq_(expect, actual)
actual = table.data().dict()
expect = {'a': 1, 'b': 2, 'c': 2}
eq_(expect, actual)
def test_teetsv():
t1 = (('foo', 'bar'),
('a', 2),
('b', 1),
('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teetsv(f1.name).selectgt('bar', 1).totsv(f2.name)
ieq(t1,
etl.fromtsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1),
etl.fromtsv(f2.name).convertnumbers())
def test_teeutsv():
t1 = (
(u'name', u'id'),
(u'Արամ Խաչատրյան', 1),
(u'Johann Strauß', 2),
(u'Вагиф Сәмәдоғлу', 3),
(u'章子怡', 4),
)
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teeutsv(f1.name).selectgt('id', 1).toutsv(f2.name)
ieq(t1, etl.fromutsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('id', 1), etl.fromutsv(f2.name).convertnumbers())
def test_valuesarray_explicit_dtype():
t = [("foo", "bar", "baz"), ("apples", 1, 2.5), ("oranges", 3, 4.4), ("pears", 7, 0.1)]
expect = np.array([1, 3, 7], dtype="i2")
actual = etl.wrap(t).values("bar").array(dtype="i2")
eq_(expect.dtype, actual.dtype)
assert np.all(expect == actual)
def test_teeutsv():
t1 = ((u'name', u'id'),
(u'Արամ Խաչատրյան', 1),
(u'Johann Strauß', 2),
(u'Вагиф Сәмәдоғлу', 3),
(u'章子怡', 4),
)
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
etl.wrap(t1).teeutsv(f1.name).selectgt('id', 1).toutsv(f2.name)
ieq(t1,
etl.fromutsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('id', 1),
etl.fromutsv(f2.name).convertnumbers())
def test_teetext():
t1 = (('foo', 'bar'), ('a', 2), ('b', 1), ('c', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
prologue = 'foo,bar\n'
template = '{foo},{bar}\n'
epilogue = 'd,4'
(etl.wrap(t1).teetext(f1.name,
template=template,
prologue=prologue,
epilogue=epilogue).selectgt('bar',
1).topickle(f2.name))
ieq(t1 + (('d', 4), ), etl.fromcsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_valuesarray_explicit_dtype():
t = [('foo', 'bar', 'baz'), ('apples', 1, 2.5), ('oranges', 3, 4.4),
('pears', 7, .1)]
expect = np.array([1, 3, 7], dtype='i2')
actual = etl.wrap(t).values('bar').array(dtype='i2')
eq_(expect.dtype, actual.dtype)
assert np.all(expect == actual)
def test_teeutext():
t1 = ((u'foo', u'bar'), (u'Արամ Խաչատրյան', 2), (u'Johann Strauß', 1),
(u'Вагиф Сәмәдоғлу', 3))
f1 = NamedTemporaryFile(delete=False)
f2 = NamedTemporaryFile(delete=False)
prologue = u'foo,bar\n'
template = u'{foo},{bar}\n'
epilogue = u'章子怡,4'
(etl.wrap(t1).teeutext(f1.name,
template=template,
prologue=prologue,
epilogue=epilogue).selectgt('bar',
1).topickle(f2.name))
ieq(t1 + ((u'章子怡', 4), ), etl.fromucsv(f1.name).convertnumbers())
ieq(etl.wrap(t1).selectgt('bar', 1), etl.frompickle(f2.name))
def test_integration():
#apidb|MAL1 ApiDB gene 56913 57116 . - . ID=apidb|PFA0035c;Name=PFA0035c;description=hypothetical+protein%2C+conserved+in+P.+falciparum;size=204;web_id=PFA0035c;locus_tag=PFA0035c;size=204;Alias=MAL1P4.06b
snps = etl.wrap((('chr', 'pos'),
('apidb|MAL1', 56911),
('apidb|MAL1', 56915)))
features = etl.fromgff3(plasmodb_gff3_file.name)
genes = features.selecteq('type', 'gene')
actual = snps.gff3join(genes, seqid='chr', start='pos', end='pos')
expect = (('chr', 'pos', 'seqid', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase', 'attributes'),
('apidb|MAL1', 56915, 'apidb|MAL1', 'ApiDB', 'gene', 56913, 57116, '.', '-', '.', gff3_parse_attributes("ID=apidb|PFA0035c;Name=PFA0035c;description=hypothetical+protein%2C+conserved+in+P.+falciparum;size=204;web_id=PFA0035c;locus_tag=PFA0035c;size=204;Alias=MAL1P4.06b")))
ieq(expect, actual)
ieq(expect, actual)
def test_integration():
left = etl.wrap((('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 = etl.wrap((('start', 'stop', 'value'),
(1, 4, 'foo'),
(3, 7, 'bar'),
(4, 9, 'baz')))
actual = left.intervaljoin(right,
lstart='begin', lstop='end',
rstart='start', rstop='stop')
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, 5, 'c', 1, 4, 'foo'),
(2, 5, 'c', 3, 7, 'bar'),
(2, 5, 'c', 4, 9, 'baz'),
(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_integration():
left = etl.wrap((('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 = etl.wrap((('start', 'stop', 'value'),
(1, 4, 'foo'),
(3, 7, 'bar'),
(4, 9, 'baz')))
actual = left.intervaljoin(right,
lstart='begin', lstop='end',
rstart='start', rstop='stop')
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, 5, 'c', 1, 4, 'foo'),
(2, 5, 'c', 3, 7, 'bar'),
(2, 5, 'c', 4, 9, 'baz'),
(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_basics():
t1 = (('foo', 'bar'), ('A', 1), ('B', 2))
w1 = etl.wrap(t1)
eq_(('foo', 'bar'), w1.header())
eq_(petl.header(w1), w1.header())
ieq((('A', 1), ('B', 2)), w1.data())
ieq(petl.data(w1), w1.data())
w2 = w1.cut('bar', 'foo')
expect2 = (('bar', 'foo'), (1, 'A'), (2, 'B'))
ieq(expect2, w2)
ieq(petl.cut(w1, 'bar', 'foo'), w2)
w3 = w1.cut('bar', 'foo').cut('foo', 'bar')
ieq(t1, w3)
def test_basics():
t1 = (('foo', 'bar'),
('A', 1),
('B', 2))
w1 = etl.wrap(t1)
eq_(('foo', 'bar'), w1.header())
eq_(petl.header(w1), w1.header())
ieq((('A', 1), ('B', 2)), w1.data())
ieq(petl.data(w1), w1.data())
w2 = w1.cut('bar', 'foo')
expect2 = (('bar', 'foo'),
(1, 'A'),
(2, 'B'))
ieq(expect2, w2)
ieq(petl.cut(w1, 'bar', 'foo'), w2)
w3 = w1.cut('bar', 'foo').cut('foo', 'bar')
ieq(t1, w3)
def test_integration():
# set up a new hdf5 table to work with
h5file = openFile("test4.h5", mode="w", title="Test file")
h5file.createGroup('/', 'testgroup', 'Test Group')
class FooBar(IsDescription):
foo = Int32Col(pos=0)
bar = StringCol(6, pos=2)
h5file.createTable('/testgroup', 'testtable', FooBar, 'Test Table')
h5file.flush()
h5file.close()
# load some initial data via tohdf5()
table1 = etl.wrap((('foo', 'bar'),
(1, 'asdfgh'),
(2, 'qwerty'),
(3, 'zxcvbn')))
table1.tohdf5('test4.h5', '/testgroup', 'testtable')
ieq(table1, etl.fromhdf5('test4.h5', '/testgroup', 'testtable'))
# append some more data
table1.appendhdf5('test4.h5', '/testgroup', 'testtable')
ieq(chain(table1, table1[1:]), etl.fromhdf5('test4.h5', '/testgroup', 'testtable'))
def test_integration():
t = etl.wrap([("foo", "bar", "baz"), ("apples", 1, 2.5), ("oranges", 3, 4.4), ("pears", 7, 0.1)])
a = t.toarray()
u = etl.fromarray(a).convert("bar", int)
ieq(t, u)
m = self.regex.match(line)
if m:
yield m.groups()
else:
raise ValueError("Failed to match regex on line: "+line)
def cachetag(self):
try:
return hash((self.source.checksum(), self.args, tuple(self.kwargs.items())))
except Exception as e:
raise Exception(e)
#
# Fluentize
#
import sys
from petl.fluent import FluentWrapper, wrap
#
# Add all of the functions in this module into the FluentWrapper as
# methods
#
for n, c in sys.modules[__name__].__dict__.items():
if callable(c):
setattr(FluentWrapper, n, wrap(c))
for line in f:
m = self.regex.match(line)
if m:
yield m.groups()
else:
raise ValueError("Failed to match regex on line: " + line)
def cachetag(self):
try:
return hash((self.source.checksum(), self.args,
tuple(self.kwargs.items())))
except Exception as e:
raise Exception(e)
#
# Fluentize
#
import sys
from petl.fluent import FluentWrapper, wrap
#
# Add all of the functions in this module into the FluentWrapper as
# methods
#
for n, c in sys.modules[__name__].__dict__.items():
if callable(c):
setattr(FluentWrapper, n, wrap(c))
def test_integration():
t = etl.wrap([('foo', 'bar', 'baz'), ('apples', 1, 2.5),
('oranges', 3, 4.4), ('pears', 7, .1)])
a = t.toarray()
u = etl.fromarray(a).convert('bar', int)
ieq(t, u)