def test_max_intron_length_filter(self):
intron_length = MaxIntronLengthFilter(30)
# Create a mock sequence
seq = Sequence()
# Give the sequence some genes
seq.genes = [
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo1'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo2'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo3')
]
# Give the mock mrnas some exon's
test_mrna0 = Mock()
test_mrna0.identifier = 'foo1-RA'
test_mrna0.death_flagged = False
test_mrna0.exon = Mock()
test_mrna0.get_shortest_intron = Mock(return_value=20)
test_mrna0.get_longest_intron = Mock(return_value=20)
test_mrna1 = Mock()
test_mrna1.identifier = 'foo2-RA'
test_mrna1.death_flagged = False
test_mrna1.exon = Mock()
test_mrna1.get_shortest_intron = Mock(return_value=30)
test_mrna1.get_longest_intron = Mock(return_value=30)
test_mrna2 = Mock()
test_mrna2.identifier = 'foo2-RB'
test_mrna2.death_flagged = False
test_mrna2.exon = None
test_mrna3 = Mock()
test_mrna3.identifier = 'foo3-RA'
test_mrna3.death_flagged = False
test_mrna3.exon = Mock()
test_mrna3.get_shortest_intron = Mock(return_value=40)
test_mrna3.get_longest_intron = Mock(return_value=40)
# Give the mock genes some mrnas
seq.genes[0].mrnas = [test_mrna0]
seq.genes[0].death_flagged = False
seq.genes[1].mrnas = [test_mrna1, test_mrna2]
seq.genes[1].death_flagged = False
seq.genes[2].mrnas = [test_mrna3]
seq.genes[2].death_flagged = False
# Apply the filter
intron_length.apply(seq)
self.assertEqual(len(seq.genes), 3)
self.assertEqual(seq.genes[0].mrnas, [test_mrna0])
self.assertEqual(seq.genes[1].mrnas, [test_mrna1, test_mrna2])
def test_max_intron_length_filter(self):
intron_length = MaxIntronLengthFilter(30)
# Create a mock sequence
seq = Sequence()
# Give the sequence some genes
seq.genes = [Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo1'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo2'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo3')]
# Give the mock mrnas some exon's
test_mrna0 = Mock()
test_mrna0.identifier = 'foo1-RA'
test_mrna0.death_flagged = False
test_mrna0.exon = Mock()
test_mrna0.get_shortest_intron = Mock(return_value=20)
test_mrna0.get_longest_intron = Mock(return_value=20)
test_mrna1 = Mock()
test_mrna1.identifier = 'foo2-RA'
test_mrna1.death_flagged = False
test_mrna1.exon = Mock()
test_mrna1.get_shortest_intron = Mock(return_value=30)
test_mrna1.get_longest_intron = Mock(return_value=30)
test_mrna2 = Mock()
test_mrna2.identifier = 'foo2-RB'
test_mrna2.death_flagged = False
test_mrna2.exon = None
test_mrna3 = Mock()
test_mrna3.identifier = 'foo3-RA'
test_mrna3.death_flagged = False
test_mrna3.exon = Mock()
test_mrna3.get_shortest_intron = Mock(return_value=40)
test_mrna3.get_longest_intron = Mock(return_value=40)
# Give the mock genes some mrnas
seq.genes[0].mrnas = [test_mrna0]
seq.genes[0].death_flagged = False
seq.genes[1].mrnas = [test_mrna1, test_mrna2]
seq.genes[1].death_flagged = False
seq.genes[2].mrnas = [test_mrna3]
seq.genes[2].death_flagged = False
# Apply the filter
intron_length.apply(seq)
self.assertEqual(len(seq.genes), 3)
self.assertEqual(seq.genes[0].mrnas, [test_mrna0])
self.assertEqual(seq.genes[1].mrnas, [test_mrna1, test_mrna2])
def test_max_cds_length_filter(self):
cds_length = MaxCDSLengthFilter(100)
# Create a mock sequence
seq = Sequence()
# Give the sequence some genes
seq.genes = [
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo1'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo2'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo3')
]
# Give the mock mrnas some cds's
test_mrna0 = Mock()
test_mrna0.identifier = 'foo1-RA'
test_mrna0.death_flagged = False
test_mrna0.cds = Mock()
test_mrna0.cds.length = Mock(return_value=90)
test_mrna1 = Mock()
test_mrna1.identifier = 'foo2-RA'
test_mrna1.death_flagged = False
test_mrna1.cds = None
test_mrna2 = Mock()
test_mrna2.identifier = 'foo2-RB'
test_mrna2.death_flagged = False
test_mrna2.cds = Mock()
test_mrna2.cds.length = Mock(return_value=100)
test_mrna3 = Mock()
test_mrna3.identifier = 'foo3-RA'
test_mrna3.death_flagged = False
test_mrna3.cds = Mock()
test_mrna3.cds.length = Mock(return_value=110)
# Give the mock genes some mrnas
seq.genes[0].mrnas = [test_mrna0]
seq.genes[0].death_flagged = False
seq.genes[1].mrnas = [test_mrna1, test_mrna2]
seq.genes[1].death_flagged = False
seq.genes[2].mrnas = [test_mrna3]
seq.genes[2].death_flagged = False
# Apply the filter
cds_length.apply(seq)
self.assertEqual(len(seq.genes), 3)
self.assertEqual(seq.genes[0].mrnas, [test_mrna0])
self.assertEqual(seq.genes[1].mrnas, [test_mrna1, test_mrna2])
def setup_seqs_and_genes(self):
self.setup_seqs()
gene1 = Mock()
gene1.seq_name = "seq2"
gene1.identifier = "gene1"
self.ctrlr.add_gene(gene1)
gene2 = Mock()
gene2.seq_name = "seq2"
gene2.identifier = "gene2"
self.ctrlr.add_gene(gene2)
gene3 = Mock()
gene3.seq_name = "seq3"
gene3.identifier = "gene3"
self.ctrlr.add_gene(gene3)
def setup_seqs_and_genes(self):
self.setup_seqs()
gene1 = Mock()
gene1.seq_name = "seq2"
gene1.identifier = "gene1"
self.ctrlr.add_gene(gene1)
gene2 = Mock()
gene2.seq_name = "seq2"
gene2.identifier = "gene2"
self.ctrlr.add_gene(gene2)
gene3 = Mock()
gene3.seq_name = "seq3"
gene3.identifier = "gene3"
self.ctrlr.add_gene(gene3)
def test_max_cds_length_filter(self):
cds_length = MaxCDSLengthFilter(100)
# Create a mock sequence
seq = Sequence()
# Give the sequence some genes
seq.genes = [Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo1'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo2'),
Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo3')]
# Give the mock mrnas some cds's
test_mrna0 = Mock()
test_mrna0.identifier = 'foo1-RA'
test_mrna0.death_flagged = False
test_mrna0.cds = Mock()
test_mrna0.cds.length = Mock(return_value=90)
test_mrna1 = Mock()
test_mrna1.identifier = 'foo2-RA'
test_mrna1.death_flagged = False
test_mrna1.cds = None
test_mrna2 = Mock()
test_mrna2.identifier = 'foo2-RB'
test_mrna2.death_flagged = False
test_mrna2.cds = Mock()
test_mrna2.cds.length = Mock(return_value=100)
test_mrna3 = Mock()
test_mrna3.identifier = 'foo3-RA'
test_mrna3.death_flagged = False
test_mrna3.cds = Mock()
test_mrna3.cds.length = Mock(return_value=110)
# Give the mock genes some mrnas
seq.genes[0].mrnas = [test_mrna0]
seq.genes[0].death_flagged = False
seq.genes[1].mrnas = [test_mrna1, test_mrna2]
seq.genes[1].death_flagged = False
seq.genes[2].mrnas = [test_mrna3]
seq.genes[2].death_flagged = False
# Apply the filter
cds_length.apply(seq)
self.assertEqual(len(seq.genes), 3)
self.assertEqual(seq.genes[0].mrnas, [test_mrna0])
self.assertEqual(seq.genes[1].mrnas, [test_mrna1, test_mrna2])
def test_add_annotations_from_list_adds_to_gene(self):
gene = Mock()
self.seq1.genes = [gene]
gene.identifier = "foo_gene"
anno_list = [["foo_gene", "name", "ABC123"], ["bar_gene", "name", "XYZ789"]]
self.seq1.add_annotations_from_list(anno_list)
self.assertEquals("ABC123", gene.name)
def add_mock_gene_with_2_mrnas(self, name):
mockgene = Mock()
mockgene.identifier = name
mockgene.death_flagged = False
mockgene.mrnas = [Mock(), Mock()]
mockgene.mrnas[0].identifier = name + "-RA"
mockgene.mrnas[0].cds = None
mockgene.mrnas[0].exon = None
mockgene.mrnas[0].length = Mock(return_value=5)
mockgene.mrnas[1].identifier = name + "-RB"
mockgene.mrnas[1].cds = Mock()
mockgene.mrnas[1].cds.identifier = [name + "-RB:CDS"]
mockgene.mrnas[1].cds.length = Mock(return_value=3)
mockgene.mrnas[1].exon = Mock()
mockgene.mrnas[1].length = Mock(return_value=2)
mockgene.get_valid_mrnas = Mock(return_value=mockgene.mrnas)
mockgene.length = Mock(return_value=10)
mockgene.get_partial_info.return_value = {
"complete": 0,
"start_no_stop": 1,
"stop_no_start": 1,
"no_stop_no_start": 1
}
mockgene.get_num_exons.return_value = 4
mockgene.get_num_introns.return_value = 3
mockgene.get_longest_exon.return_value = 10
mockgene.get_longest_intron.return_value = 10
mockgene.get_shortest_exon.return_value = 5
mockgene.get_shortest_intron.return_value = 5
mockgene.get_total_exon_length.return_value = 25
mockgene.get_total_intron_length.return_value = 25
self.seq1.add_gene(mockgene)
def test_add_mrna_annotation(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
self.test_gene0.mrnas = [mrna]
self.test_gene0.add_mrna_annotation("foo_mrna", "gag_flag",
"awesome_anno")
mrna.add_annotation.assert_called_with("gag_flag", "awesome_anno")
def test_add_annotations_from_list_adds_to_gene(self):
gene = Mock()
self.seq1.genes = [gene]
gene.identifier = "foo_gene"
anno_list = [["foo_gene", "name", "ABC123"], ["bar_gene", "name", "XYZ789"]]
self.seq1.add_annotations_from_list(anno_list)
self.assertEquals("ABC123", gene.name)
def add_mock_gene_with_2_mrnas(self, name):
mockgene = Mock()
mockgene.indices = [20, 30]
mockgene.identifier = name
mockgene.death_flagged = False
mockgene.mrnas = [Mock(), Mock()]
mockgene.mrnas[0].identifier = name + "-RA"
mockgene.mrnas[0].cds = None
mockgene.mrnas[0].exon = None
mockgene.mrnas[0].length = Mock(return_value=5)
mockgene.mrnas[1].identifier = name + "-RB"
mockgene.mrnas[1].cds = Mock()
mockgene.mrnas[1].cds.identifier = [name + "-RB:CDS"]
mockgene.mrnas[1].cds.length = Mock(return_value=3)
mockgene.mrnas[1].exon = Mock()
mockgene.mrnas[1].length = Mock(return_value=2)
mockgene.get_valid_mrnas = Mock(return_value=mockgene.mrnas)
mockgene.length = Mock(return_value=10)
mockgene.get_partial_info.return_value = {
"complete": 0,
"start_no_stop": 1,
"stop_no_start": 1,
"no_stop_no_start": 1,
}
mockgene.get_num_exons.return_value = 4
mockgene.get_num_introns.return_value = 3
mockgene.get_longest_exon.return_value = 10
mockgene.get_longest_intron.return_value = 10
mockgene.get_shortest_exon.return_value = 5
mockgene.get_shortest_intron.return_value = 5
mockgene.get_total_exon_length.return_value = 25
mockgene.get_total_intron_length.return_value = 25
self.seq1.add_gene(mockgene)
def test_mrna_to_protein_fasta_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '-'
expected = ">foo_mrna protein\nCNL*\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '-'
expected = ">foo_mrna protein\nCNL*\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_fasta_reverse_strand(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_cds_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna CDS\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_cds_fasta(mrna))
def test_mrna_to_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '+'
expected = ">foo_mrna\nGATTACAgattaca\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_fasta_reverse_strand(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_cds_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna CDS\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_cds_fasta(mrna))
def test_mrna_to_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '+'
expected = ">foo_mrna\nGATTACAgattaca\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_protein_fasta_phase1(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.cds.get_phase.return_value = 1
mrna.strand = '+'
expected = ">foo_mrna protein\nITDY\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_get_sequence_from_indices_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '-'
expected = 'TGTAATCtgtaatc'
calculated = self.helper.get_sequence_from_indices(mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_mrna_to_protein_fasta_phase1(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.cds.get_phase.return_value = 1
mrna.strand = '+'
expected = ">foo_mrna protein\nITDY\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_get_sequence_from_indices(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '+'
expected = 'gattacaGATTACA'
calculated = self.helper.get_sequence_from_indices(mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_get_sequence_from_indices_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '-'
expected = 'TGTAATCtgtaatc'
calculated = self.helper.get_sequence_from_indices(
mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def add_mock_gene(self, name="foo_gene"):
mockgene = Mock()
mockgene.identifier = name
mockgene.indices = [2, 4]
mockgene.death_flagged = False
mockgene.to_mrna_fasta.return_value = "mockgene_to_mrna_fasta\n"
mockgene.to_cds_fasta.return_value = "mockgene_to_cds_fasta\n"
mockgene.to_protein_fasta.return_value = "mockgene_to_protein_fasta\n"
mockgene.get_valid_mrnas = Mock(return_value=[])
self.seq1.add_gene(mockgene)
def test_add_annotations_from_list_adds_to_mrna(self):
gene = Mock()
mrna = Mock()
self.seq1.genes = [gene]
gene.mrnas = [mrna]
gene.identifier = "foo_gene"
gene.contains_mrna.return_value = True
anno_list = [["foo_mrna", "Dbxref", "PFAM:0001"]]
self.seq1.add_annotations_from_list(anno_list)
gene.add_mrna_annotation.assert_called_with("foo_mrna", "Dbxref", "PFAM:0001")
def test_get_sequence_from_indices(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '+'
expected = 'gattacaGATTACA'
calculated = self.helper.get_sequence_from_indices(
mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_add_annotations_from_list_adds_to_mrna(self):
gene = Mock()
mrna = Mock()
self.seq1.genes = [gene]
gene.mrnas = [mrna]
gene.identifier = "foo_gene"
gene.contains_mrna.return_value = True
anno_list = [["foo_mrna", "Dbxref", "PFAM:0001"]]
self.seq1.add_annotations_from_list(anno_list)
gene.add_mrna_annotation.assert_called_with("foo_mrna", "Dbxref", "PFAM:0001")
def add_mock_gene(self, name="foo_gene"):
mockgene = Mock()
mockgene.identifier = name
mockgene.indices = [2, 4]
mockgene.death_flagged = False
mockgene.to_mrna_fasta.return_value = "mockgene_to_mrna_fasta\n"
mockgene.to_cds_fasta.return_value = "mockgene_to_cds_fasta\n"
mockgene.to_protein_fasta.return_value = "mockgene_to_protein_fasta\n"
mockgene.get_valid_mrnas = Mock(return_value=[])
self.seq1.add_gene(mockgene)
def test_custom_date_field_widget(self):
obj = Mock()
obj.prefix = "objprefix"
obj.identifier= "objident"
obj.htmlAttributes = {}
obj.valueType = "medium"
request = TestRequest()
form = Form(obj, request)
form.prefix="form.prefix"
datefield = DateFieldWidget(obj, form, request)
datum = datetime.date(2011,01,01)
def test_custom_date_field_widget(self):
obj = Mock()
obj.prefix = "objprefix"
obj.identifier = "objident"
obj.htmlAttributes = {}
obj.valueType = "medium"
request = TestRequest()
form = Form(obj, request)
form.prefix = "form.prefix"
datefield = DateFieldWidget(obj, form, request)
datum = datetime.date(2011, 01, 01)
def test_parse_exclude_images_commands():
"""Test for namesake function"""
commands = [["1:101:200"], ["0:201:300"]]
ranges = _parse_exclude_images_commands(commands, [])
assert ranges == [("1", (101, 200)), ("0", (201, 300))]
experiments = ["1", "2"]
short_command = [["101:200"]]
with pytest.raises(ValueError):
_ = _parse_exclude_images_commands(short_command, experiments)
mock_exp = Mock()
mock_exp.identifier = "1"
ranges = _parse_exclude_images_commands(short_command, [mock_exp])
assert ranges == [("1", (101, 200))]
with pytest.raises(ValueError):
_ = _parse_exclude_images_commands([["1:101-200"]], [mock_exp])
with pytest.raises(ValueError):
_ = _parse_exclude_images_commands([["1:101:a"]], [])
def test_parse_exclude_images_commands():
"""Test for namesake function"""
commands = [["1:101:200"], ["0:201:300"]]
r1 = flex.reflection_table()
r1.experiment_identifiers()[1] = "1"
r0 = flex.reflection_table()
r0.experiment_identifiers()[0] = "0"
tables = [r0, r1]
ranges = _parse_exclude_images_commands(commands, [], tables)
assert ranges == [("1", (101, 200)), ("0", (201, 300))]
experiments = ["1", "2"]
short_command = [["101:200"]]
with pytest.raises(ValueError):
_ = _parse_exclude_images_commands(short_command, experiments, tables)
mock_exp = Mock()
mock_exp.identifier = "1"
ranges = _parse_exclude_images_commands(short_command, [mock_exp], tables)
assert ranges == [("1", (101, 200))]
with pytest.raises(ValueError):
_ = _parse_exclude_images_commands([["1:101-200"]], [mock_exp], tables)
with pytest.raises(ValueError):
_ = _parse_exclude_images_commands([["1:101:a"]], [], tables)
def test_add_mrna_annotation(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
self.test_gene0.mrnas = [mrna]
self.test_gene0.add_mrna_annotation("foo_mrna", "gag_flag", "awesome_anno")
mrna.add_annotation.assert_called_with("gag_flag", "awesome_anno")
