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()