def test_remove_low_cov_links(self):
'''test _remove_low_cov_links'''
ref_lengths = {'ref1': 100, 'ref2': 200, 'ref3': 300}
g = scaffold_graph.Graph(ref_lengths)
g.contig_links = {
('ref1', 'ref2'): {
'LR': 42,
'RL': 41
},
('ref2', 'ref3'): {
'LR': 43,
'RL': 42
},
('ref3', 'ref4'): {
'LR': 1,
'RL': 2
}
}
g._remove_low_cov_links(42)
expected = {
('ref1', 'ref2'): {
'LR': 42
},
('ref2', 'ref3'): {
'LR': 43,
'RL': 42
}
}
self.assertDictEqual(expected, g.contig_links)
def test_update_from_sam(self):
'''test update_from_sam'''
sam_reader = pysam.Samfile(
os.path.join(data_dir, 'graph_test_update_from_sam.bam'), "rb")
ref_lengths = {}
pyfastaq.tasks.lengths_from_fai(
os.path.join(data_dir, 'graph_test_update_from_sam.ref.fa.fai'),
ref_lengths)
graph = scaffold_graph.Graph(ref_lengths)
for sam in sam_reader.fetch(until_eof=True):
graph.update_from_sam(sam, sam_reader)
self.assertEqual(len(graph.partial_links), 0)
self.assertEqual(len(graph.links), 1)
key = ('ref1', 'ref2')
self.assertTrue(key in graph.links)
expected_links = [
link.Link(None,
None,
None,
s='\t'.join([
'ref1', '506', 'R', '300', 'ref2', '500', 'L', '359'
]))
]
self.assertListEqual(graph.links[key], expected_links)
def __init__(self, bam, ref_seqs):
'''Construct a Parser.
bam: name of BAM file
ref_seqs: dictionary of sequence name => Fasta object'''
self.bam = os.path.abspath(bam)
self.soft_clipped = {}
self.ref_lengths = {seq: len(ref_seqs[seq]) for seq in ref_seqs}
self.scaff_graph = scaffold_graph.Graph(self.ref_lengths)
self.unmapped_mates = {}
self.sam_reader = pysam.Samfile(self.bam, "rb")
def test_contig_graph_is_consistent(self):
'''test _contig_graph_is_consistent'''
ref_lengths = {'ref1': 100, 'ref2': 200, 'ref3': 300}
g = scaffold_graph.Graph(ref_lengths)
good_links = [
{
('ref1', 'ref2'): {
'RL': 42
}
},
{
('ref1', 'ref2'): {
'RL': 42
},
('ref2', 'ref3'): {
'RL': 42
}
},
]
bad_links = [{
('ref1', 'ref2'): {
'LR': 42,
'RL': 42
}
}, {
('ref1', 'ref2'): {
'LR': 42
},
('ref1', 'ref3'): {
'LR': 42
}
}]
for d in good_links:
g.contig_links = d
self.assertTrue(g._contig_graph_is_consistent())
for d in bad_links:
g.contig_links = d
self.assertFalse(g._contig_graph_is_consistent())
def test_make_graph(self):
'''test _make_graph'''
ref_lengths = {'ref1': 100, 'ref2': 200, 'ref3': 300}
g = scaffold_graph.Graph(ref_lengths)
g.partial_links = {42: 42}
with self.assertRaises(scaffold_graph.Error):
g._make_graph(1000)
g.partial_links = {}
g.links[('ref1', 'ref2')] = [
link.Link(
None, None, None,
'\t'.join(['ref1', '100', 'R', '50', 'ref2', '200', 'L',
'10']))
]
g._make_graph(10)
self.assertEqual(len(g.contig_links), 0)
g._make_graph(1000)
self.assertEqual(len(g.contig_links), 1)
expected_contig_links = {('ref1', 'ref2'): {'RL': 1}}
self.assertDictEqual(g.contig_links, expected_contig_links)
g.links[('ref1', 'ref2')].append(
link.Link(
None, None, None,
'\t'.join(['ref1', '100', 'R', '50', 'ref2', '200', 'L',
'10'])))
g.links[('ref1', 'ref2')].append(
link.Link(
None, None, None,
'\t'.join(['ref1', '100', 'L', '50', 'ref2', '200', 'R',
'10'])))
g._make_graph(1000)
expected_contig_links = {('ref1', 'ref2'): {'RL': 2, 'LR': 1}}
self.assertDictEqual(g.contig_links, expected_contig_links)
def test_write_all_links_to_file(self):
'''test write_all_links_to_file'''
ref_lengths = {'ref1': 100, 'ref2': 200, 'ref3': 300}
g = scaffold_graph.Graph(ref_lengths)
g.links[('ref1', 'ref2')] = [
link.Link(
None, None, None,
'\t'.join(['ref1', '100', 'R', '50', 'ref2', '200', 'L',
'10']))
]
g.links[('ref1', 'ref2')].append(
link.Link(
None, None, None,
'\t'.join(['ref1', '100', 'R', '50', 'ref2', '200', 'L',
'10'])))
g.links[('ref1', 'ref2')].append(
link.Link(
None, None, None,
'\t'.join(['ref1', '100', 'L', '50', 'ref2', '200', 'R',
'10'])))
g.links[('ref3', 'ref4')] = [
link.Link(
None, None, None,
'\t'.join(['ref3', '100', 'R', '42', 'ref4', '200', 'L',
'42']))
]
tmp_file = 'tmp.contig_links'
g.write_all_links_to_file(tmp_file)
self.assertTrue(
filecmp.cmp(os.path.join(data_dir,
'graph_test_write_all_links_to_file.out'),
tmp_file,
shallow=False))
os.unlink(tmp_file)