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Marco Lenoir
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[0473b3]: / tests / test_gindexer.py

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import os



import matplotlib

import numpy as np

import pkg_resources

import pytest

import pandas as pd



from janggu.data import GenomicIndexer



matplotlib.use('AGG')



def test_gindexer_short_interval():

    data_path = pkg_resources.resource_filename('janggu', 'resources/')





    gi = GenomicIndexer.create_from_file(os.path.join(data_path,

                                                 'sample_equalsize.bed'),

                                    binsize=200, stepsize=200)

    assert len(gi) == 4

    gi = GenomicIndexer.create_from_file(os.path.join(data_path,

                                                 'sample_equalsize.bed'),

                                    binsize=180, stepsize=20)

    assert len(gi) == 8

    gi = GenomicIndexer.create_from_file(os.path.join(data_path,

                                                 'sample_equalsize.bed'),

                                    binsize=210, stepsize=20, zero_padding=False)

    assert len(gi) == 0



    gi = GenomicIndexer.create_from_file(os.path.join(data_path,

                                                 'sample_equalsize.bed'),

                                    binsize=210, stepsize=20, zero_padding=True)

    assert len(gi) == 4





def test_gindexer_short_interval_with_dataframe():

    data_path = pkg_resources.resource_filename('janggu', 'resources/')

    df = pd.read_csv(os.path.join(data_path, 'sample_equalsize.bed'),

                     sep='\t', header=None, names=['chrom', 'start', 'end'])



    gi = GenomicIndexer.create_from_file(df,

                                         binsize=200, stepsize=200)

    assert len(gi) == 4

    gi = GenomicIndexer.create_from_file(df,

                                         binsize=180, stepsize=20)

    assert len(gi) == 8

    gi = GenomicIndexer.create_from_file(df,

                                         binsize=210, stepsize=20,

                                         zero_padding=False)

    assert len(gi) == 0



    gi = GenomicIndexer.create_from_file(df,

                                         binsize=210, stepsize=20,

                                         zero_padding=True)

    assert len(gi) == 4





def test_gindexer_errors():

    data_path = pkg_resources.resource_filename('janggu', 'resources/')



    with pytest.raises(ValueError):

        GenomicIndexer.create_from_file(os.path.join(data_path,

                                                     'sample.bed'),

                                        binsize=0, stepsize=50)



    with pytest.raises(ValueError):

        GenomicIndexer.create_from_file(os.path.join(data_path,

                                                     'sample.bed'),

                                        binsize=10, stepsize=0)

    with pytest.raises(ValueError):

        # due to flank < 0

        GenomicIndexer.create_from_file(os.path.join(data_path, 'sample.bed'),

                                        binsize=200, stepsize=50, flank=-1)

    # due to unequal intervals

    gi=GenomicIndexer.create_from_file(os.path.join(data_path, 'scores.bed'),

                                    binsize=None, stepsize=None, flank=0)

    #print(len(gi))

    #for reg in gi:

    #    print(reg)

    GenomicIndexer.create_from_file(os.path.join(data_path, 'scores.bed'),

                                    binsize=200, stepsize=200, flank=0)



def test_gindexer_merged():

    data_path = pkg_resources.resource_filename('janggu', 'resources/')



    gi = GenomicIndexer.create_from_file(

        os.path.join(data_path, 'sample.bed'), binsize=200, stepsize=200)

    np.testing.assert_equal(len(gi), 100)

    gi2 = gi.filter_by_region(include='chr1')

    gi3 = gi.filter_by_region(include='chr10')

    gi4 = gi.filter_by_region(exclude='chr2')

    gi5 = gi.filter_by_region(exclude='chr10')





    np.testing.assert_equal(len(gi2), 50)



    np.testing.assert_equal(len(gi3), 0)

    np.testing.assert_equal(len(gi4), 50)

    np.testing.assert_equal(len(gi5), 100)





def test_gindexer_merged_variable_length_ranges():

    data_path = pkg_resources.resource_filename('janggu', 'resources/')



    # with fixed size

    gi = GenomicIndexer.create_from_file(

        os.path.join(data_path, 'sample.bed'), binsize=3000, stepsize=3000,

        zero_padding=False)

    np.testing.assert_equal(len(gi), 6)



    iv = gi[0]

    np.testing.assert_equal((iv.chrom, iv.start, iv.end, iv.strand),

                            ('chr1', 15000, 18000, '+'))

    iv = gi[-1]

    np.testing.assert_equal((iv.chrom, iv.start, iv.end, iv.strand),

                            ('chr2', 21000, 24000, '-'))



    # with variable size regions

    gi = GenomicIndexer.create_from_file(

        os.path.join(data_path, 'sample.bed'), binsize=3000,

        stepsize=3000, zero_padding=True)

    np.testing.assert_equal(len(gi), 8)



    iv = gi[0]

    np.testing.assert_equal((iv.chrom, iv.start, iv.end, iv.strand),

                            ('chr1', 15000, 18000, '+'))

    iv = gi[-1]

    np.testing.assert_equal((iv.chrom, iv.start, iv.end, iv.strand),

                            ('chr2', 24000, 25000, '-'))