def test_create_ob_graph(self):
run_argument_parser([
"create_ob_graph", "-o", "tests/testgraph.obg",
"tests/vg_test_graph.json"
])
graph = GraphWithReversals.from_numpy_file("tests/testgraph.obg")
self.assertEqual(graph, self.correct_ob_graph)
def test_concatenate_fasta_files(self):
if os.path.isfile("out.fasta"):
os.remove("out.fasta")
file1 = open("1_sequences.fasta", "w")
peak1 = Peak(3, 5, [1], score=3)
peak1_header = ">peak1 " + peak1.to_file_line() + "\n"
file1.writelines([peak1_header])
file1.writelines(["AACC\n"])
file1.close()
file2 = open("2_sequences.fasta", "w")
peak2 = Peak(2, 5, [1], score=7)
peak2_header = ">peak2 " + peak2.to_file_line() + "\n"
file2.writelines([peak2_header])
file2.writelines(["CCAA\n"])
file2.close()
run_argument_parser(["concatenate_sequence_files", "1,2", "out.fasta"])
outfile = open("out.fasta")
lines = list(outfile.readlines())
self.assertEqual(Peak.from_file_line(lines[0].split(maxsplit=1)[1]),
peak2)
self.assertEqual(Peak.from_file_line(lines[2].split(maxsplit=1)[1]),
peak1)
outfile.close()
def test_split_vg_alignments(self):
run_argument_parser([
"split_vg_json_reads_into_chromosomes", "1,2,3,4,5",
"tests/node_range_test_data/vg_alignments.json",
"tests/node_range_test_data/"
])
for chrom in ["1", "2", "3", "4", "5"]:
f = open("tests/node_range_test_data/vg_alignments_" + chrom +
".json")
self.assertEqual(len(f.readlines()), 3)
f.close()
def test_typical_run(self):
print(" ========= Running start ====")
run_argument_parser([
"callpeaks", "-g", "*.nobg", "-s",
"test_sample_*.intervalcollection", "-f",
"%s" % self.fragment_length, "-r",
"%s" % self.read_length, "-u", "100", "-G", "150", "-n",
"multigraphs_", "-p", "True", "-D", "True"
])
for i, chromosome in enumerate(self.chromosomes):
run_argument_parser([
"callpeaks_whole_genome_from_p_values", chromosome, "-d", "./",
"-f",
"%s" % self.fragment_length, "-r",
"%s" % self.read_length, "-n", "multigraphs_"
])
self.do_asserts()
def test_intervals_to_fasta_from_fasta(self):
run_argument_parser([
"create_ob_graph", "-o", "tests/testgraph.obg",
"tests/vg_test_graph.json"
])
PeakCollection([Peak(0, 2, [1, 2], score=3)
]).to_file("tests/testintervals.intervalcollection",
text_file=True)
run_argument_parser([
"peaks_to_fasta", "tests/testgraph.obg.sequences",
"tests/testintervals.intervalcollection",
"tests/testsequences.fasta"
])
collection = PeakCollection.from_fasta_file(
"tests/testsequences.fasta")
self.assertEqual(len(collection.intervals), 1)
self.assertEqual(collection.intervals[0].sequence.lower(), "tttcccctt")
def test_get_summits(self):
qvalues = SparseValues(np.array([0]), np.array([3]))
qvalues.track_size = 22
qvalues.to_sparse_files("tests/test_qvalues")
run_argument_parser([
"create_ob_graph", "-o", "tests/testgraph.obg",
"tests/vg_test_graph.json"
])
max_paths = PeakCollection([Peak(0, 2, [1, 2], score=3)])
PeakFasta(self.correct_sequence_graph).write_max_path_sequences(
"tests/test_max_paths.fasta", max_paths)
run_argument_parser([
"get_summits", "-g", "tests/testgraph.obg",
"tests/test_max_paths.fasta", "tests/test_qvalues", "2"
])
result = PeakCollection.from_fasta_file(
"tests/test_max_paths_summits.fasta")
self.assertEqual(result.intervals[0], Peak(2, 6, [1]))
self.assertEqual(result.intervals[0].sequence.lower(), "tccc")
def test_all_steps(self):
run_argument_parser([
"create_ob_graph", "-o", "tests/testgraph.obg",
"tests/vg_test_graph.json"
])
run_argument_parser(
['create_linear_map', "--graph", "tests/testgraph.obg"])
IntervalCollection([Interval(1, 1, [1, 2])
]).to_file("tests/sample.intervalcollection")
run_argument_parser([
"callpeaks", "--graph", "tests/testgraph.obg", "-s",
"tests/sample.intervalcollection", "-n", "tests/test_experiment_",
"-f", "10", "-r", "7"
])
def _test_multigraph(self):
run_argument_parser([
"callpeaks_whole_genome", "--chromosomes", "--graph",
"tests/testgraph.obg", "-s", "tests/sample.intervalcollection",
"-n", "tests/test_experiment_", "-f", "10", "-r", "7"
])