import pytest import sys import os import glob import sysconfig from pathlib import Path import unittest import pytest import conftest # build_dir = "build/lib.%s-%s" % (sysconfig.get_platform(), sys.version[0:3]) # sys.path.insert(0, os.path.join(os.getcwd(), build_dir)) import HTSeq try: import pyBigWig except ImportError: pyBigWig = None data_folder = conftest.get_data_folder() class TestGenomicInterval(unittest.TestCase): def test_init(self): iv = HTSeq.GenomicInterval( "chr1", 100, 200, ".", ) class TestChromVector(unittest.TestCase): def test_init_step(self): # Autoallocation cv = HTSeq.ChromVector.create( HTSeq.GenomicInterval("chr1", 100, 200, "."), typecode="d", storage="step", ) def test_init_stretch(self): # Autoallocation cv = HTSeq.ChromVector.create( HTSeq.GenomicInterval("chr1", 100, 200, "."), typecode="d", storage="stretch", ) def test_steps_stretch(self): cv = HTSeq.ChromVector.create( HTSeq.GenomicInterval("chr1", 100, 200, "."), typecode="d", storage="stretch", ) cv[120:130] = 45 cv[129:140] = 89 cv[180:182] = 1 steps = list(cv.steps()) self.assertEqual(steps[0][0], HTSeq.GenomicInterval("chr1", 120, 129)) self.assertEqual(steps[1][0], HTSeq.GenomicInterval("chr1", 129, 140)) self.assertEqual(steps[2][0], HTSeq.GenomicInterval("chr1", 180, 182)) self.assertEqual(steps[0][1], 45) self.assertEqual(steps[1][1], 89) self.assertEqual(steps[2][1], 1) class TestGenomicArray(unittest.TestCase): def test_init(self): # Autoallocation ga = HTSeq.GenomicArray("auto") # Infinite length chromosomes ga = HTSeq.GenomicArray(["1", "2"]) # Fixed chromosomes ga = HTSeq.GenomicArray( { "1": 5898, "2": 4876, } ) # Store: ndarray ga = HTSeq.GenomicArray( { "1": 5898, "2": 4876, }, storage="ndarray", ) # Store: memmap ga = HTSeq.GenomicArray( { "1": 5898, "2": 4876, }, storage="memmap", memmap_dir=".", ) def test_steps(self): for storage in ["step", "ndarray"]: ga = HTSeq.GenomicArray( { "1": 5898, "2": 4876, }, storage=storage, ) steps = ga.steps() steps_exp = [ (HTSeq.GenomicInterval("1", 0, 5898, strand="+"), 0), (HTSeq.GenomicInterval("1", 0, 5898, strand="-"), 0), (HTSeq.GenomicInterval("2", 0, 4876, strand="+"), 0), (HTSeq.GenomicInterval("2", 0, 4876, strand="-"), 0), ] for step, step_exp in zip(steps, steps_exp): self.assertEqual(step, step_exp) def test_access_out_of_range(self): """Ensure chromosomes are made with infinite size, which can be accessed""" def _get_arrays(): return { "Provided chrom": HTSeq.GenomicArray(["1"], typecode="O"), "Auto chrom": HTSeq.GenomicArray("auto", typecode="O"), } # Test we can access unknown regions without error unknown_iv = HTSeq.GenomicInterval("1", 200, 300, "+") for name, genomic_array in _get_arrays().items(): step = list(genomic_array[unknown_iv].steps())[0] unknown_value = step[1] self.assertIsNone(unknown_value, msg="Access unknown in " + name) # Test accessing unknown regions works the same even if we call setter first known_iv = HTSeq.GenomicInterval("1", 0, 100, strand="+") for name, genomic_array in _get_arrays().items(): # Call setter first before getter genomic_array[known_iv] = "test" step = list(genomic_array[unknown_iv].steps())[0] unknown_value = step[1] self.assertIsNone( unknown_value, msg="Access unknown after calling setter in " + name ) def test_bedgraph(self): def compare_bedgraph_line(line1, line2): fields1 = line1.split() fields2 = line2.split() # Chromosome self.assertEqual(fields1[0], fields2[0]) # Start-end self.assertEqual(int(fields1[1]), int(fields2[1])) self.assertEqual(int(fields1[2]), int(fields2[2])) # Value self.assertEqual(float(fields1[3]), float(fields2[3])) ga = HTSeq.GenomicArray.from_bedgraph_file( data_folder + "example_bedgraph.bedgraph", strand=".", ) steps = [] for iv, value in ga.steps(): steps.append((iv.chrom, iv.start, iv.end, value)) steps_exp = [ ("chr19", 49302000, 49302300, -1.0), ("chr19", 49302300, 49302600, -0.75), ("chr19", 49302600, 49302900, -0.50), ("chr19", 49302900, 49303200, -0.25), ("chr19", 49303200, 49303500, 0.0), ("chr19", 49303500, 49303800, 0.25), ("chr19", 49303800, 49304100, 0.50), ("chr19", 49304100, 49304400, 0.75), ("chr19", 49304400, 49304700, 1.00), ] self.assertEqual(steps, steps_exp) ga.write_bedgraph_file( "test_output.bedgraph", track_options='name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20', separator=" ", ) with ( open(data_folder + "example_bedgraph.bedgraph") as f1, open("test_output.bedgraph") as f2, ): header_found = False for line1, line2 in zip(f1, f2): if not header_found: self.assertEqual(line1, line2) else: compare_bedgraph_line(line1, line2) if "track type" in line1: header_found = True @unittest.skipIf(pyBigWig is None, "test case depends on pyBigWig") def test_bigwig(self): ga = HTSeq.GenomicArray.from_bigwig_file( data_folder + "example_bigwig.bw", ) ga.write_bigwig_file( "test_output.bw", ) import pyBigWig with ( pyBigWig.open(data_folder + "example_bigwig.bw") as bw1, pyBigWig.open("test_output.bw") as bw2, ): self.assertEqual(bw1.chroms(), bw2.chroms()) for chrom in bw1.chroms(): self.assertEqual( bw1.intervals(chrom), bw2.intervals(chrom), ) def test_access_out_of_range(self): """Ensure chromosomes are made with infinite size, which can be accessed""" def _get_arrays(): return { "Provided chrom": HTSeq.GenomicArray(["1"], typecode="O"), "Auto chrom": HTSeq.GenomicArray("auto", typecode="O"), } # Test we can access unknown regions without error unknown_iv = HTSeq.GenomicInterval("1", 200, 300, "+") for name, genomic_array in _get_arrays().items(): step = list(genomic_array[unknown_iv].steps())[0] unknown_value = step[1] self.assertIsNone(unknown_value, msg="Access unknown in " + name) # Test accessing unknown regions works the same even if we call setter first known_iv = HTSeq.GenomicInterval("1", 0, 100, strand="+") for name, genomic_array in _get_arrays().items(): # Call setter first before getter genomic_array[known_iv] = "test" step = list(genomic_array[unknown_iv].steps())[0] unknown_value = step[1] self.assertIsNone( unknown_value, msg="Access unknown after calling setter in " + name ) if __name__ == "__main__": suite = TestGenomicArray() suite.test_init()