def test_to_dict(self):
"""
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
r = Report('redfang')
a = Attribute('a', 'b')
a2 = Attribute('a2', 'b2')
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup('pgid')
pg.add_plot(Plot('pid', 'anImg'))
pg.add_plot(Plot('pid2', 'anImg2'))
r.add_plotgroup(pg)
t = Table('tabid')
t.add_column(Column('c1'))
r.add_table(t)
d = r.to_dict()
log.debug("\n" + pformat(d))
self.assertEqual('redfang', d['id'])
self.assertEqual('redfang.a', d['attributes'][0]['id'])
self.assertEqual('redfang.a2', d['attributes'][1]['id'])
self.assertEqual('redfang.pgid', d['plotGroups'][0]['id'])
self.assertEqual('redfang.pgid.pid', d['plotGroups'][0]['plots'][0]['id'])
self.assertEqual('redfang.pgid.pid2', d['plotGroups'][0]['plots'][1]['id'])
self.assertEqual('redfang.tabid', d['tables'][0]['id'])
self.assertEqual('redfang.tabid.c1', d['tables'][0]['columns'][0]['id'])
def test_to_dict_multi(self):
"""
Multiple complex elements.
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
tags = ["alpha", "beta", "gamma"]
r = Report('redfang', tags=tags)
a = Attribute('a', 'b')
a2 = Attribute('a2', 'b2')
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup('pgid')
pg.add_plot(Plot('pid', 'anImg'))
pg.add_plot(Plot('pid2', 'anImg2'))
r.add_plotgroup(pg)
pg = PlotGroup('pgid2')
pg.add_plot(Plot('pid2', 'anImg2'))
pg.add_plot(Plot('pid22', 'anImg22'))
r.add_plotgroup(pg)
t = Table('tabid')
t.add_column(Column('c1'))
r.add_table(t)
t = Table('tabid2')
t.add_column(Column('c2'))
r.add_table(t)
d = r.to_dict()
log.debug(str(d))
assert 'redfang' == d['id']
assert 'redfang.a' == d['attributes'][0]['id']
assert 'redfang.a2' == d['attributes'][1]['id']
assert 'redfang.pgid' == d['plotGroups'][0]['id']
assert 'redfang.pgid.pid' == d['plotGroups'][0]['plots'][0]['id']
assert 'redfang.pgid.pid2' == d['plotGroups'][0]['plots'][1]['id']
assert 'redfang.pgid2' == d['plotGroups'][1]['id']
assert 'redfang.pgid2.pid2' == d['plotGroups'][1]['plots'][0]['id']
assert 'redfang.pgid2.pid22' == d['plotGroups'][1]['plots'][1]['id']
assert 'redfang.tabid' == d['tables'][0]['id']
assert 'redfang.tabid.c1' == d['tables'][0]['columns'][0]['id']
assert 'redfang.tabid2' == d['tables'][1]['id']
assert 'redfang.tabid2.c2' == d['tables'][1]['columns'][0]['id']
assert list(sorted(d['tags'])) == list(sorted(tags))
loaded_report = load_report_from(d)
assert list(sorted(loaded_report.tags)) == list(sorted(tags))
log.info(repr(r))
assert repr(r) is not None
def test_to_dict_multi(self):
"""
Multiple complex elements.
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
r = Report('redfang')
a = Attribute('a', 'b')
a2 = Attribute('a2', 'b2')
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup('pgid')
pg.add_plot(Plot('pid', 'anImg'))
pg.add_plot(Plot('pid2', 'anImg2'))
r.add_plotgroup(pg)
pg = PlotGroup('pgid2')
pg.add_plot(Plot('pid2', 'anImg2'))
pg.add_plot(Plot('pid22', 'anImg22'))
r.add_plotgroup(pg)
t = Table('tabid')
t.add_column(Column('c1'))
r.add_table(t)
t = Table('tabid2')
t.add_column(Column('c2'))
r.add_table(t)
d = r.to_dict()
log.debug(str(d))
self.assertEqual('redfang', d['id'])
self.assertEqual('redfang.a', d['attributes'][0]['id'])
self.assertEqual('redfang.a2', d['attributes'][1]['id'])
self.assertEqual('redfang.pgid', d['plotGroups'][0]['id'])
self.assertEqual('redfang.pgid.pid', d[
'plotGroups'][0]['plots'][0]['id'])
self.assertEqual('redfang.pgid.pid2', d[
'plotGroups'][0]['plots'][1]['id'])
self.assertEqual('redfang.pgid2', d['plotGroups'][1]['id'])
self.assertEqual('redfang.pgid2.pid2', d[
'plotGroups'][1]['plots'][0]['id'])
self.assertEqual('redfang.pgid2.pid22', d[
'plotGroups'][1]['plots'][1]['id'])
self.assertEqual('redfang.tabid', d['tables'][0]['id'])
self.assertEqual('redfang.tabid.c1', d['tables'][
0]['columns'][0]['id'])
self.assertEqual('redfang.tabid2', d['tables'][1]['id'])
self.assertEqual('redfang.tabid2.c2', d[
'tables'][1]['columns'][0]['id'])
log.info(repr(r))
self.assertIsNotNone(repr(r))
def test_to_dict_multi(self):
"""
Multiple complex elements.
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
r = Report('redfang')
a = Attribute('a', 'b')
a2 = Attribute('a2', 'b2')
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup('pgid')
pg.add_plot(Plot('pid', 'anImg'))
pg.add_plot(Plot('pid2', 'anImg2'))
r.add_plotgroup(pg)
pg = PlotGroup('pgid2')
pg.add_plot(Plot('pid2', 'anImg2'))
pg.add_plot(Plot('pid22', 'anImg22'))
r.add_plotgroup(pg)
t = Table('tabid')
t.add_column(Column('c1'))
r.add_table(t)
t = Table('tabid2')
t.add_column(Column('c2'))
r.add_table(t)
d = r.to_dict()
log.debug(str(d))
self.assertEqual('redfang', d['id'])
self.assertEqual('redfang.a', d['attributes'][0]['id'])
self.assertEqual('redfang.a2', d['attributes'][1]['id'])
self.assertEqual('redfang.pgid', d['plotGroups'][0]['id'])
self.assertEqual('redfang.pgid.pid',
d['plotGroups'][0]['plots'][0]['id'])
self.assertEqual('redfang.pgid.pid2',
d['plotGroups'][0]['plots'][1]['id'])
self.assertEqual('redfang.pgid2', d['plotGroups'][1]['id'])
self.assertEqual('redfang.pgid2.pid2',
d['plotGroups'][1]['plots'][0]['id'])
self.assertEqual('redfang.pgid2.pid22',
d['plotGroups'][1]['plots'][1]['id'])
self.assertEqual('redfang.tabid', d['tables'][0]['id'])
self.assertEqual('redfang.tabid.c1',
d['tables'][0]['columns'][0]['id'])
self.assertEqual('redfang.tabid2', d['tables'][1]['id'])
self.assertEqual('redfang.tabid2.c2',
d['tables'][1]['columns'][0]['id'])
log.info(repr(r))
self.assertIsNotNone(repr(r))
def test_to_dict(self):
"""
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
r = Report("redfang")
a = Attribute("a", "b")
a2 = Attribute("a2", "b2")
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup("pgid")
pg.add_plot(Plot("pid", "anImg"))
pg.add_plot(Plot("pid2", "anImg2"))
r.add_plotgroup(pg)
t = Table("tabid")
t.add_column(Column("c1"))
r.add_table(t)
d = r.to_dict()
log.debug("\n" + pformat(d))
self.assertEqual("redfang", d["id"])
self.assertEqual("redfang.a", d["attributes"][0]["id"])
self.assertEqual("redfang.a2", d["attributes"][1]["id"])
self.assertEqual("redfang.pgid", d["plotGroups"][0]["id"])
self.assertEqual("redfang.pgid.pid", d["plotGroups"][0]["plots"][0]["id"])
self.assertEqual("redfang.pgid.pid2", d["plotGroups"][0]["plots"][1]["id"])
self.assertEqual("redfang.tabid", d["tables"][0]["id"])
self.assertEqual("redfang.tabid.c1", d["tables"][0]["columns"][0]["id"])
def test_get_table_by_id_with_bad_id(self):
r = Report('redfang')
t1 = Table('tabid1')
t1.add_column(Column('c1'))
r.add_table(t1)
bad_t = r.get_table_by_id('id_that_does_not_exist')
self.assertIsNone(bad_t)
def test_get_table_by_id(self):
r = Report('redfang')
t1 = Table('tabid1')
t1.add_column(Column('c1'))
r.add_table(t1)
t = r.get_table_by_id('tabid1')
self.assertEqual(t, t1)
def test_get_table_by_id_with_bad_id(self):
r = Report('redfang')
t1 = Table('tabid1')
t1.add_column(Column('c1'))
r.add_table(t1)
bad_t = r.get_table_by_id('id_that_does_not_exist')
self.assertIsNone(bad_t)
def test_get_table_by_id(self):
r = Report('redfang')
t1 = Table('tabid1')
t1.add_column(Column('c1'))
r.add_table(t1)
t = r.get_table_by_id('tabid1')
self.assertEqual(t, t1)
def test_get_column_by_id(self):
r = Report('redfang')
t1 = Table('tabid1')
c1 = Column('c1')
t1.add_column(c1)
r.add_table(t1)
c = r.get_table_by_id('tabid1').get_column_by_id('c1')
self.assertEqual(c, c1)
def test_get_column_by_id(self):
r = Report('redfang')
t1 = Table('tabid1')
c1 = Column('c1')
t1.add_column(c1)
r.add_table(t1)
c = r.get_table_by_id('tabid1').get_column_by_id('c1')
self.assertEqual(c, c1)
def test_get_column_by_id_with_bad_id(self):
r = Report('redfang')
t1 = Table('tabid1')
c1 = Column('c1')
t1.add_column(c1)
r.add_table(t1)
bad_c = r.get_table_by_id('tabid1').get_column_by_id(
'id_that_does_not_exist')
assert bad_c is None
def test_get_table_by_id(self):
r = Report('redfang')
t1 = Table('tabid1')
t1.add_column(Column('c1'))
r.add_table(t1)
t = r.get_table_by_id('tabid1')
assert t == t1
columns_d = t.to_columns_d()
assert len(columns_d) == 0
def test_to_dict_multi(self):
"""
Multiple complex elements.
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
r = Report("redfang")
a = Attribute("a", "b")
a2 = Attribute("a2", "b2")
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup("pgid")
pg.add_plot(Plot("pid", "anImg"))
pg.add_plot(Plot("pid2", "anImg2"))
r.add_plotgroup(pg)
pg = PlotGroup("pgid2")
pg.add_plot(Plot("pid2", "anImg2"))
pg.add_plot(Plot("pid22", "anImg22"))
r.add_plotgroup(pg)
t = Table("tabid")
t.add_column(Column("c1"))
r.add_table(t)
t = Table("tabid2")
t.add_column(Column("c2"))
r.add_table(t)
d = r.to_dict()
log.debug(str(d))
self.assertEqual("redfang", d["id"])
self.assertEqual("redfang.a", d["attributes"][0]["id"])
self.assertEqual("redfang.a2", d["attributes"][1]["id"])
self.assertEqual("redfang.pgid", d["plotGroups"][0]["id"])
self.assertEqual("redfang.pgid.pid", d["plotGroups"][0]["plots"][0]["id"])
self.assertEqual("redfang.pgid.pid2", d["plotGroups"][0]["plots"][1]["id"])
self.assertEqual("redfang.pgid2", d["plotGroups"][1]["id"])
self.assertEqual("redfang.pgid2.pid2", d["plotGroups"][1]["plots"][0]["id"])
self.assertEqual("redfang.pgid2.pid22", d["plotGroups"][1]["plots"][1]["id"])
self.assertEqual("redfang.tabid", d["tables"][0]["id"])
self.assertEqual("redfang.tabid.c1", d["tables"][0]["columns"][0]["id"])
self.assertEqual("redfang.tabid2", d["tables"][1]["id"])
self.assertEqual("redfang.tabid2.c2", d["tables"][1]["columns"][0]["id"])
log.info(repr(r))
self.assertIsNotNone(repr(r))
def test_to_dict(self):
"""
The id of report sub elements is prepended with the id of the parent
element when to_dict is called.
"""
r = Report('redfang')
a = Attribute('a', 'b')
a2 = Attribute('a2', 'b2')
r.add_attribute(a)
r.add_attribute(a2)
pg = PlotGroup('pgid')
pg.add_plot(Plot('pid', 'anImg'))
pg.add_plot(Plot('pid2', 'anImg2'))
r.add_plotgroup(pg)
t = Table('tabid')
t.add_column(Column('c1'))
r.add_table(t)
d = r.to_dict()
log.debug("\n" + pformat(d))
r2 = load_report_from(d)
self.assertEqual(r.uuid, r2.uuid)
self.assertEqual('redfang', d['id'])
self.assertEqual('redfang.a', d['attributes'][0]['id'])
self.assertEqual('redfang.a2', d['attributes'][1]['id'])
self.assertEqual('redfang.pgid', d['plotGroups'][0]['id'])
self.assertEqual('redfang.pgid.pid',
d['plotGroups'][0]['plots'][0]['id'])
self.assertEqual('redfang.pgid.pid2',
d['plotGroups'][0]['plots'][1]['id'])
self.assertEqual('redfang.tabid', d['tables'][0]['id'])
self.assertEqual('redfang.tabid.c1',
d['tables'][0]['columns'][0]['id'])
def _get_consensus_table_and_attributes(ref_data, reference_entry):
"""
Get a tuple: Table and list of Attributes
:param ref_data: (dict) dict of data pulled from alignment_summary.gff
:param reference_entry: (pbsystem.io.reference_entry) reference entry
:return: tuple (pbreports.io.model.Table, [pbreports.io.model.Attributes])
"""
table = Table('consensus_table', 'Consensus Calling Results')
table.add_column(Column('contig_name', 'Reference'))
table.add_column(Column('contig_len', 'Reference Length'))
table.add_column(Column('bases_called', 'Bases Called'))
table.add_column(Column('concordance', 'Consensus Accuracy'))
table.add_column(Column('coverage', 'Base Coverage'))
ordered_ids = _ref_ids_ordered_by_len(ref_data)
sum_lengths = 0.0
mean_bases_called = 0
mean_concord = 'NA'
mean_coverage = 0
for seqid in ordered_ids:
contig = reference_entry.get_contig(seqid)
length = float(ref_data[seqid][LENGTH])
gaps = float(ref_data[seqid][GAPS])
errors = float(ref_data[seqid][ERR])
cov = float(ref_data[seqid][COV])
sum_lengths += length
bases_called = 1.0 - gaps / length
mean_bases_called += bases_called * length
concord = 'NA'
if length != gaps:
log.info('length {f}'.format(f=length))
log.info('gaps {f}'.format(f=gaps))
log.info('errors {f}'.format(f=errors))
concord = 1.0 - errors / (length - gaps)
if mean_concord is 'NA':
mean_concord = concord * length
else:
mean_concord += concord * length
coverage = cov / length
mean_coverage += coverage * length
# table shows values for each contig
table.add_data_by_column_id('contig_name', contig.name)
table.add_data_by_column_id('contig_len', length)
table.add_data_by_column_id('bases_called', bases_called)
table.add_data_by_column_id('concordance', concord)
table.add_data_by_column_id('coverage', coverage)
mean_contig_length = sum_lengths / len(ordered_ids)
mean_bases_called = mean_bases_called / sum_lengths
if mean_concord is not 'NA':
mean_concord = mean_concord / sum_lengths
mean_coverage = mean_coverage / sum_lengths
attributes = [Attribute(id_, val, Constants.ATTR_LABELS[id_])
for id_, val in [
(Constants.MEAN_CONTIG_LENGTH, mean_contig_length),
(Constants.MEAN_BASES_CALLED, mean_bases_called),
(Constants.MEAN_CONCORDANCE, mean_concord),
(Constants.MEAN_COVERAGE, mean_coverage),
(Constants.LONGEST_CONTIG, ordered_ids[0])]]
return table, attributes
