def test_write_json_no_info(self):
"""correctly writes an object with out an info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
mock = patch("data.source", autospec=True)
mock.to_rich_dict = DNA.to_rich_dict
mock.source = join("blah", "delme.json")
writer = io_app.write_json(outdir, create=True)
_ = writer(mock)
reader = io_app.load_json()
got = reader(writer.data_store[0])
self.assertEqual(got, DNA)
# now with a zipped archive
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme.zip")
mock = patch("data.source", autospec=True)
mock.to_rich_dict = DNA.to_rich_dict
mock.source = join("blah", "delme.json")
writer = io_app.write_json(outdir, create=True)
identifier = writer(mock)
reader = io_app.load_json()
# checking loadable from a data store member too
got = reader(writer.data_store[0])
self.assertEqual(got, DNA)
expect = join(outdir.replace(".zip", ""), "delme.json")
if expect.startswith("." + os.sep):
expect = expect[2:]
self.assertEqual(identifier, expect)
def test_load_json(self):
"""correctly loads an object from json"""
from cogent3.app.data_store import make_record_for_json
data = make_record_for_json("delme", DNA, True)
data = json.dumps(data)
# straight directory
with TemporaryDirectory(dir=".") as dirname:
outpath = join(dirname, "delme.json")
with open(outpath, "w") as outfile:
outfile.write(data)
reader = io_app.load_json()
got = reader(outpath)
self.assertIsInstance(got, DNA.__class__)
self.assertEqual(got, DNA)
# zipped directory
with TemporaryDirectory(dir=".") as dirname:
zip_path = join(dirname, "delme.zip")
outpath = "delme/delme.json"
with zipfile.ZipFile(zip_path, "a") as out:
out.writestr(outpath, data)
dstore = io_app.get_data_store(zip_path, suffix="json")
member = dstore.get_member("delme.json")
reader = io_app.load_json()
got = reader(member)
self.assertIsInstance(got, DNA.__class__)
self.assertEqual(got, DNA)
def test_write_json_with_info(self):
"""correctly writes an object with info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
from cogent3.app.result import generic_result
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
obj = generic_result(source=join("blah", "delme.json"))
obj["dna"] = DNA
writer = io_app.write_json(outdir, create=True)
_ = writer(obj)
reader = io_app.load_json()
got = reader(join(outdir, "delme.json"))
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
# now with a zipped archive
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme.zip")
obj = generic_result(source=join("blah", "delme.json"))
obj["dna"] = DNA
writer = io_app.write_json(outdir, create=True)
identifier = writer(obj)
reader = io_app.load_json()
got = reader(writer.data_store[0])
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
expect = join(outdir.replace(".zip", ""), "delme.json")
if expect.startswith("." + os.sep):
expect = expect[2:]
self.assertEqual(identifier, expect)
def test_write_json_with_info(self):
"""correctly writes an object with info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
from cogent3.util.union_dict import UnionDict
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
mock = Mock()
mock.to_rich_dict = DNA.to_rich_dict
mock.info = UnionDict(source=join("blah", "delme.json"))
writer = io_app.write_json(outdir, create=True)
_ = writer(mock)
reader = io_app.load_json()
got = reader(join(outdir, "delme.json"))
self.assertEqual(got, DNA)
# now with a zipped archive
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme.zip")
mock = Mock()
mock.to_rich_dict = DNA.to_rich_dict
mock.info = UnionDict(source=join("blah", "delme.json"))
writer = io_app.write_json(outdir, create=True)
identifier = writer(mock)
reader = io_app.load_json()
got = reader(writer.data_store[0])
self.assertEqual(got, DNA)
expect = join(outdir.replace(".zip", ""), "delme.json")
if expect.startswith("." + os.sep):
expect = expect[2:]
self.assertEqual(identifier, expect)
def test_write_json_no_info(self):
"""correctly writes an object with out an info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
gr = _get_generic_result(join("blah", "delme.json"))
writer = io_app.write_json(outdir, create=True)
_ = writer(gr)
reader = io_app.load_json()
got = reader(writer.data_store[0])
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
def test_write_json_with_info(self):
"""correctly writes an object with info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
from cogent3.app.result import generic_result
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
obj = generic_result(source=join("blah", "delme.json"))
obj["dna"] = DNA
writer = io_app.write_json(outdir, create=True)
_ = writer(obj)
reader = io_app.load_json()
got = reader(join(outdir, "delme.json"))
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
"""
Display a Phylogenetic Tree Showing Bootstrap Support
=====================================================
We use a tree saved in `json` format from a 100 replicate bootstrap resamplings. The `show_support=True` argument controls whether or not to display support. The `threshold=0.8` argument indicates only nodes with a support level ≤0.8 will have support text displayed.
"""
# %%
from cogent3.app import io
reader = io.load_json()
tree = reader("../../data/tree-with-support.json")
fig = tree.get_figure(show_support=True, threshold=0.8)
fig.scale_bar = None
fig.show(width=500, height=400)
#%%
# Change the placement of support text
# ####################################
#
# The support text is positioned relative to the `x`, `y` coordinates of the tree node. Control over support text placement is achieved using the `support_xshift` and `support_yshift` attributes. These are expressed in terms of pixels.
#
# To place the support text internal to the node, we set the yshift=0 (so at the same y-value of the node) and xshift it to the right using a positive integer.
fig.support_xshift = 15
fig.support_yshift = 0
fig.show(width=500, height=400)
"""
Dotplot with annotated sequences
================================
If sequences in a dotplot have been annotated, the `dotplot()` method returns an `AnnotatedDrawable`.
"""
#%%
# Reloading from json
# ###################
#
# The data file, `tp53.json`, was created from a query of ensembl for one-to-one orthologs of human TP53 between Human, Macaque, Orangutan and Marmoset. The resulting sequences were annotated with the location of the CDS for the canonical transcript, then the `SequenceCollection` was saved as json using `cogent3.app.write_json`.
from cogent3.app.io import get_data_store, load_json
loader = load_json()
seqs = loader("../../data/tp53.json")
dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600)
dp.show()
#%%
# Removing annotation tracks
# ##########################
help(dp.remove_track)
#%%
# Thus we could remove the left annotation track, for instance with
#
# ```python
# dp.remove_track(left_track=True)
# ```
