def test_bw(): b = BigWig("libBigWig/test/test.bw") assert repr(b) == "BigWig('libBigWig/test/test.bw')" intervals = list(b("1", 0, 99)) assert intervals[0] == Interval(chrom='1', start=0, end=1, value=0.10000000149011612) assert intervals[1] == Interval(chrom='1', start=1, end=2, value=0.20000000298023224) assert intervals[2] == Interval(chrom='1', start=2, end=3, value=0.30000001192092896) # default is to include all values vals = b.values("1", 0, 9) exp = array('f', [0.10000000149011612, 0.20000000298023224, 0.30000001192092896, nan, nan, nan, nan, nan, nan]) arr_equal(vals, exp) vals = b.values("1", 0, 9, False) exp = array('f', [0.10000000149011612, 0.20000000298023224, 0.30000001192092896]) arr_equal(vals, exp) v = b.stats("1", 0, 9) assert v == 0.2000000054637591 v = b.stats("1", 0, 9, stat="stdev") assert v == 0.10000000521540645 v = b.stats("1", 0, 4, stat="coverage") assert v == 0.75 v = b.stats("1", 0, 4, stat="coverage", nBins=2) assert v == array('d', [1.0, 0.5]) b.close()
def read_gerp(region, sends, path='/scratch/ucgd/lustre/u1021864/serial/hg19.gerp.bw'): gerp = BigWig(path) exongerp=[] chrom, se = region.split(":") s, e = map(int, se.split("-")) if not chrom.startswith("chr"): chrom = "chr" + chrom for key in sends: for (exs, exe) in zip(sends[key][0], sends[key][1]): exongerp.extend(np.frombuffer(gerp.values(chrom, int(exs)-1, int(exe)), dtype='f')) return np.frombuffer(gerp.values(chrom, int(s)-1, int(e)), dtype='f'), exongerp
def test_bw(): b = BigWig("libBigWig/test/test.bw") assert repr(b) == "BigWig('libBigWig/test/test.bw')" intervals = list(b("1", 0, 99)) assert intervals[0] == Interval(chrom='1', start=0, end=1, value=0.10000000149011612) assert intervals[1] == Interval(chrom='1', start=1, end=2, value=0.20000000298023224) assert intervals[2] == Interval(chrom='1', start=2, end=3, value=0.30000001192092896) # default is to include all values vals = b.values("1", 0, 9) exp = array('f', [ 0.10000000149011612, 0.20000000298023224, 0.30000001192092896, nan, nan, nan, nan, nan, nan ]) arr_equal(vals, exp) vals = b.values("1", 0, 9, False) exp = array( 'f', [0.10000000149011612, 0.20000000298023224, 0.30000001192092896]) arr_equal(vals, exp) v = b.stats("1", 0, 9) assert v == 0.2000000054637591 v = b.stats("1", 0, 9, stat="stdev") assert v == 0.10000000521540645 v = b.stats("1", 0, 4, stat="coverage") assert v == 0.75 v = b.stats("1", 0, 4, stat="coverage", nBins=2) assert v == array('d', [1.0, 0.5]) b.close()
def test_bad_chr(): b = BigWig("libBigWig/test/test.bw") assert b.stats("chr1", 0, 10) is None v = b.values("chr1", 0, 10) assert len(v) == 0, v