def recordtree(table, start='start', stop='stop'):
"""
Construct an interval tree for the given table, where each node in the tree is a row of the table represented
as a hybrid tuple/dictionary-style record object.
"""
try:
import bx.intervals
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
getstart = attrgetter(start)
getstop = attrgetter(stop)
tree = bx.intervals.intersection.IntervalTree()
for rec in records(table):
tree.add(getstart(rec), getstop(rec), rec)
def recordtree(table, start='start', stop='stop'):
"""
Construct an interval tree for the given table, where each node in the tree is a row of the table represented
as a hybrid tuple/dictionary-style record object.
"""
try:
import bx.intervals
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
getstart = attrgetter(start)
getstop = attrgetter(stop)
tree = bx.intervals.intersection.IntervalTree()
for rec in records(table):
tree.add(getstart(rec), getstop(rec), rec)
def test_records_unevenrows():
table = (('foo', 'bar'), ('a', 1, True), ('b',))
actual = records(table)
# access items
it = iter(actual)
o = it.next()
eq_('a', o['foo'])
eq_(1, o['bar'])
o = it.next()
eq_('b', o['foo'])
eq_(None, o['bar'])
# access attributes
it = iter(actual)
o = it.next()
eq_('a', o.foo)
eq_(1, o.bar)
o = it.next()
eq_('b', o.foo)
eq_(None, o.bar)
def test_records():
table = (('foo', 'bar'), ('a', 1), ('b', 2))
actual = records(table)
# access items
it = iter(actual)
o = it.next()
eq_('a', o['foo'])
eq_(1, o['bar'])
o = it.next()
eq_('b', o['foo'])
eq_(2, o['bar'])
# access attributes
it = iter(actual)
o = it.next()
eq_('a', o.foo)
eq_(1, o.bar)
o = it.next()
eq_('b', o.foo)
eq_(2, o.bar)
def recordtrees(table, facet, start='start', stop='stop'):
"""
Construct faceted interval trees for the given table, where each node in the tree is a row of the table represented
as a hybrid tuple/dictionary-style record object.
"""
try:
import bx.intervals
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
getstart = attrgetter(start)
getstop = attrgetter(stop)
getkey = attrgetter(facet)
trees = dict()
for rec in records(table):
k = getkey(rec)
if k not in trees:
trees[k] = bx.intervals.intersection.IntervalTree()
trees[k].add(getstart(rec), getstop(rec), rec)
return trees
def recordtrees(table, facet, start='start', stop='stop'):
"""
Construct faceted interval trees for the given table, where each node in the tree is a row of the table represented
as a hybrid tuple/dictionary-style record object.
"""
try:
import bx.intervals
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
getstart = attrgetter(start)
getstop = attrgetter(stop)
getkey = attrgetter(facet)
trees = dict()
for rec in records(table):
k = getkey(rec)
if k not in trees:
trees[k] = bx.intervals.intersection.IntervalTree()
trees[k].add(getstart(rec), getstop(rec), rec)
return trees
def tojson(table, source=None, *args, **kwargs):
"""
Write a table in JSON format. E.g.::
>>> from petl import tojson, look
>>> look(table)
+-------+-------+
| 'foo' | 'bar' |
+=======+=======+
| 'a' | 1 |
+-------+-------+
| 'b' | 2 |
+-------+-------+
| 'c' | 2 |
+-------+-------+
>>> tojson(table, 'example.json')
>>> # check what it did
... import json
>>> with open('example.json') as f:
... json.load(f)
...
[{u'foo': u'a', u'bar': 1}, {u'foo': u'b', u'bar': 2}, {u'foo': u'c', u'bar': 2}]
Note that this is currently not streaming, all data is loaded into memory
before being written to the file.
.. versionadded:: 0.5
"""
encoder = JSONEncoder(*args, **kwargs)
source = _write_source_from_arg(source)
with source.open_('wb') as f:
for chunk in encoder.iterencode(list(records(table))):
f.write(chunk)
