def test_create_histogram(self):
     """
     Simple (non null) test of histogram
     """
     tcs = get_top_contigs(self.REFERENCE, 25)
     als = self.GFF
     pls = _get_contigs_to_plot(als, tcs)
     stats = _get_reference_coverage_stats(pls.values())
     fig, ax = _create_histogram(stats)
     self.assertIsNotNone(fig)
     self.assertIsNotNone(ax)
 def test_get_coverage_stats(self):
     """
     Test the coverage stats object (needs more)
     """
     tcs = get_top_contigs(self.REFERENCE, 25)
     als = self.GFF
     pls = _get_contigs_to_plot(als, tcs)
     contig = tcs[0]
     c_cov = pls[contig.header]
     stats = _get_reference_coverage_stats(pls.values())
     self.assertEqual(485, len(stats.means))
 def test_get_coverage_stats(self):
     """
     Test the coverage stats object (needs more)
     """
     ref = os.path.join(self._data_dir, 'references', 'lambda')
     tcs = get_top_contigs(ref, 25)
     als = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
     pls = _get_contigs_to_plot(als, tcs)
     contig = tcs[0]
     c_cov = pls[contig.header]
     stats = _get_reference_coverage_stats(pls.values())
     self.assertEqual(485, len(stats.means))
    def test_create_histogram(self):
        """
        Simple (non null) test of histogram
        """
        ref = os.path.join(self._data_dir, 'references', 'lambda')
        tcs = get_top_contigs(ref, 25)
        als = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
        pls = _get_contigs_to_plot(als, tcs)

        stats = _get_reference_coverage_stats(pls.values())

        fig, ax = _create_histogram(stats)
        self.assertIsNotNone(fig)
        self.assertIsNotNone(ax)
 def test_create_coverage_histo_plot_grp(self):
     """
     Test that plotGroup of the histogram is created as expected
     """
     tcs = get_top_contigs(self.REFERENCE, 25)
     als = self.GFF
     pls = _get_contigs_to_plot(als, tcs)
     stats = _get_reference_coverage_stats(pls.values())
     plot_group = _create_coverage_histo_plot_grp(stats, self._output_dir)
     # only 1 histo
     self.assertEqual(1, len(plot_group.plots))
     self._assert_image_file(plot_group.thumbnail)
     for plot in plot_group.plots:
         self._assert_image_file(plot.image)
 def test_attributes_high_coverage(self):
     tcs = get_top_contigs(self.REFERENCE, 25)
     als = op.join(self._data_dir, "alignment_summary.lambda.gff")
     pls = _get_contigs_to_plot(als, tcs)
     contig = tcs[0]
     c_cov = pls[contig.header]
     stats = _get_reference_coverage_stats(pls.values())
     att = _get_att_mean_coverage(stats)
     # This was in coverage.xml for the alignment summary gff used
     # attribute hidden="true" id="depth_coverage_mean" name="Coverage"
     # value="2958.16">2958.16</attribute>
     self.assertAlmostEqual(2958.16, att.value, places=2)
     att = _get_att_percent_missing(stats)
     self.assertEqual(0, att.value)
 def test_attributes(self):
     """
     Test that attribute values match expected
     """
     tcs = get_top_contigs(self.REFERENCE, 25)
     als = self.GFF
     pls = _get_contigs_to_plot(als, tcs)
     contig = tcs[0]
     c_cov = pls[contig.header]
     stats = _get_reference_coverage_stats(pls.values())
     att = _get_att_mean_coverage(stats)
     # This was in coverage.xml for the alignment summary gff used
     # attribute hidden="true" id="depth_coverage_mean" name="Coverage"
     # value="2958.16">2958.16</attribute>
     self.assertAlmostEqual(1.228, att.value, places=3)
     att = _get_att_percent_missing(stats)
     self.assertAlmostEqual(58.4, att.value, places=1)
    def test_create_coverage_histo_plot_grp(self):
        """
        Test that plotGroup of the histogram is created as expected
        """

        ref = os.path.join(self._data_dir, 'references', 'lambda')
        tcs = get_top_contigs(ref, 25)
        als = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
        pls = _get_contigs_to_plot(als, tcs)
        stats = _get_reference_coverage_stats(pls.values())

        plot_group = _create_coverage_histo_plot_grp(stats, self._output_dir)

        # only 1 histo
        self.assertEqual(1, len(plot_group.plots))
        self._assert_image_file(plot_group.thumbnail)

        for plot in plot_group.plots:
            self._assert_image_file(plot.image)
    def test_attributes(self):
        """
        Test that attribute values match expected
        """
        ref = os.path.join(self._data_dir, 'references', 'lambda')
        tcs = get_top_contigs(ref, 25)
        als = os.path.join(self._data_dir, 'alignment_summary.lambda.gff')
        pls = _get_contigs_to_plot(als, tcs)
        contig = tcs[0]
        c_cov = pls[contig.header]
        stats = _get_reference_coverage_stats(pls.values())
        att = _get_att_mean_coverage(stats)
        # This was in coverage.xml for the alignment summary gff used
        # attribute hidden="true" id="depth_coverage_mean" name="Coverage" value="2958.16">2958.16</attribute>

        self.assertEqual(2958.1640346377467, att.value)

        att = _get_att_percent_missing(stats)
        self.assertEqual(0, att.value)