示例#1
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文件: test.py 项目: liuhui9312/tadbit
def main():
    """
    main function
    """
    chrom = argv[0]
    chrom = 'chrT/chrT_A.tsv'
    chrom = get_matrix(chrom)

    out = tadbit(chrom, verbose=True, heuristic=True)
    print('{:>6} ' * len(out[0])).format(*out[0])
    print('{:>6.1f} ' * len(out[1])).format(*out[1])

    plt.imshow(log2(chrom.T), origin='lower')
    plt.vlines(out[0], 0, chrom.shape[0])
    plt.hlines(out[0], 0, chrom.shape[0])
    plt.show()

    chrom_path = 'chrT/'
    out_batch = batch_tadbit(chrom_path, n_cpus=1, heuristic=True)
    print('{:>6} ' * len(out_batch[0])).format(*out_batch[0])
    print('{:>6.1f} ' * len(out_batch[1])).format(*out_batch[1])

    plt.imshow(log2(chrom.T), origin='lower')
    plt.vlines(out[0], 0, chrom.shape[0])
    plt.hlines(out[0], 0, chrom.shape[0])
    plt.vlines(out_batch[0], 0, chrom.shape[0], color='red')
    plt.hlines(out_batch[0], 0, chrom.shape[0], color='red')
    plt.show()
示例#2
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文件: test.py 项目: rdacemel/TADbit
def main():
    """
    main function
    """
    chrom = argv[0]
    chrom = "chrT/chrT_A.tsv"
    chrom = get_matrix(chrom)

    out = tadbit(chrom, verbose=True, heuristic=True)
    print("{:>6} " * len(out[0])).format(*out[0])
    print("{:>6.1f} " * len(out[1])).format(*out[1])

    plt.imshow(log2(chrom.T), origin="lower")
    plt.vlines(out[0], 0, chrom.shape[0])
    plt.hlines(out[0], 0, chrom.shape[0])
    plt.show()

    chrom_path = "chrT/"
    out_batch = batch_tadbit(chrom_path, n_cpus=1, heuristic=True)
    print("{:>6} " * len(out_batch[0])).format(*out_batch[0])
    print("{:>6.1f} " * len(out_batch[1])).format(*out_batch[1])

    plt.imshow(log2(chrom.T), origin="lower")
    plt.vlines(out[0], 0, chrom.shape[0])
    plt.hlines(out[0], 0, chrom.shape[0])
    plt.vlines(out_batch[0], 0, chrom.shape[0], color="red")
    plt.hlines(out_batch[0], 0, chrom.shape[0], color="red")
    plt.show()
示例#3
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 def test_02_batch_tadbit(self):
     global batch_exp
     batch_exp= batch_tadbit('20Kb/chrT/', max_tad_size=20, verbose=False,
                             no_heuristic=True)
     breaks = [0, 4, 9, 15, 20, 29, 36, 44, 50, 62, 67, 76, 90, 95]
     scores = [4.0, 7.0, 3.0, 7.0, 4.0, 4.0, 6.0, 7.0, 10.0, 10.0,
               8.0, 9.0, 7.0, None]
     self.assertEqual(batch_exp['start'], breaks)
     self.assertEqual(batch_exp['score'], scores)
示例#4
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    def test_02_batch_tadbit(self):
        if ONLY and ONLY != "02":
            return
        if CHKTIME:
            t0 = time()

        global batch_exp
        batch_exp = batch_tadbit(PATH + "/20Kb/chrT/", max_tad_size=20, verbose=False, no_heuristic=True)
        # Breaks and scores with square root normalization.
        breaks = [0, 4, 14, 19, 34, 39, 44, 50, 62, 67, 72, 90, 95]
        scores = [4.0, 6.0, 5.0, 5.0, 4.0, 8.0, 5.0, 4.0, 6.0, 5.0, 6.0, 6.0, None]
        self.assertEqual(batch_exp["start"], breaks)
        self.assertEqual(batch_exp["score"], scores)
        if CHKTIME:
            print "2", time() - t0
示例#5
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    def test_02_batch_tadbit(self):
        if CHKTIME:
            t0 = time()

        global batch_exp
        batch_exp = batch_tadbit(PATH + '/20Kb/chrT/', max_tad_size=20, 
                                 verbose=False, no_heuristic=True)
        # Breaks and scores with square root normalization.
        breaks = [0, 4, 14, 19, 34, 39, 44, 50, 62, 67, 72, 90, 95]
        scores = [4.0, 6.0, 5.0, 5.0, 4.0, 8.0, 5.0, 4.0, 6.0, 5.0,
                  6.0, 6.0, None]
        self.assertEqual(batch_exp['start'], breaks)
        self.assertEqual(batch_exp['score'], scores)
        if CHKTIME:
            print '2', time() - t0
示例#6
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    def test_02_batch_tadbit(self):
        if CHKTIME:
            t0 = time()

        global batch_exp
        batch_exp = batch_tadbit(PATH + '/20Kb/chrT/', max_tad_size=20, 
                                 verbose=False, no_heuristic=True)
        # Breaks and scores with square root normalization.
        #breaks = [0, 4, 9, 15, 20, 29, 36, 44, 50, 62, 67, 76, 90, 95]
        #scores = [4.0, 7.0, 4.0, 8.0, 4.0, 4.0, 7.0, 7.0, 10.0, 10.0, 9.0, 8.0, 7.0, None]
        breaks = [0, 4, 14, 19, 34, 44, 50, 62, 67, 72, 90, 95]
        scores = [4.0, 6.0, 6.0, 6.0, 6.0, 6.0, 5.0, 6.0, 4.0, 6.0, 5.0, None]
        self.assertEqual(batch_exp['start'], breaks)
        self.assertEqual(batch_exp['score'], scores)
        if CHKTIME:
            print '2', time() - t0
示例#7
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 def test_batch_tadbit(self):
     out = batch_tadbit("chrT/", max_tad_size=20, verbose=False, no_heuristic=True)
     breaks = [0, 3, 9, 14, 20, 36, 41, 46, 51, 56, 62, 67, 74, 79, 84]
     scores = [8.0, 10.0, 7.0, 7.0, 5.0, 5.0, 7.0, 7.0, 9.0, 10.0, 10.0, 5.0, 3.0, 6.0, None]
     self.assertEqual(out["start"], breaks)
     self.assertEqual(out["score"], scores)