Python remap.sam_to_conseqs函数代码示例

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本文整理汇总了Python中micall.core.remap.sam_to_conseqs函数的典型用法代码示例。如果您正苦于以下问题：Python sam_to_conseqs函数的具体用法？Python sam_to_conseqs怎么用？Python sam_to_conseqs使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。

在下文中一共展示了sam_to_conseqs函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。

示例1: testDebugReportsOnReverseRead

    def testDebugReportsOnReverseRead(self):
        sam_file = StringIO(
            "@SQ\tSN:test\n"
            "test1\t99\ttest\t1\t44\t3M3I2M\t=\t1\t8\tACTGGGAG\tJJJJJJJJ\n"
            "test1\t147\ttest\t5\t44\t8M\t=\t1\t-8\tGACCCAAC\tJJJJJIJJ\n"
            "test1\t99\ttest\t1\t44\t3M3I2M\t=\t1\t12\tATTGGGAG\tJJJJJJJJ\n"
            "test1\t147\ttest\t5\t44\t8M\t=\t1\t-12\tGACCCAAC\tJJJJJHJJ\n"
        )
        reports = {('test', 10): None}
        expected_reports = {('test', 10): 'H{A: 2}, I{A: 1}'}

        remap.sam_to_conseqs(sam_file, debug_reports=reports)

        self.assertDictEqual(expected_reports, reports)

开发者ID:cfe-lab，项目名称:MiCall，代码行数:14，代码来源:test_remap.py

示例2: testDebugReports

    def testDebugReports(self):
        sam_file = StringIO(
            "@SQ\tSN:test\n"
            "test1\t99\ttest\t1\t44\t3M3I9M\t=\t1\t12\tACTGGGAGACCCAAC\tJIJJJJJJJJJJJJJ\n"
            "test1\t147\ttest\t1\t44\t3M3I9M\t=\t1\t-12\tACTGGGAGACCCAAC\tJIJJJJJJJJJJJJJ\n"
            "test1\t99\ttest\t1\t44\t3M3I9M\t=\t1\t12\tATTGGGAGACCCAAC\tJHJJJJJJJJJJJJJ\n"
            "test1\t147\ttest\t1\t44\t3M3I9M\t=\t1\t-12\tATTGGGAGACCCAAC\tJHJJJJJJJJJJJJJ\n"
        )
        reports = {('test', 2): None}
        expected_reports = {('test', 2): 'H{C: 1, T: 1}, I{C: 1}'}

        remap.sam_to_conseqs(sam_file, debug_reports=reports)

        self.assertDictEqual(expected_reports, reports)

开发者ID:cfe-lab，项目名称:MiCall，代码行数:14，代码来源:test_remap.py

示例3: testSeedsConverged

    def testSeedsConverged(self):
        # SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
        sam_file = StringIO(
            "@SQ\tSN:test\tSN:other\tSN:wayoff\n"
            "test1\t99\ttest\t1\t44\t10M\t=\t1\t10\tATGAGGAGTA\tJJJJJJJJJJJJ\n"
            "other1\t99\tother\t1\t44\t10M\t=\t1\t10\tATGACCAGTA\tJJJJJJJJJJJJ\n"
            "wayoff1\t99\twayoff\t1\t44\t10M\t=\t1\t10\tATGAGGGTAC\tJJJJJJJJJJJJ\n"
        )
        seeds = {'test': 'ATGAAGTA',
                 'other': 'AAGCCGAA',
                 'wayoff': 'TCATGTAC'}
        expected_conseqs = {'test': 'ATGAGGAGTA'}
        expected_distances = {'test': dict(seed_dist=2,
                                           other_dist=5,
                                           other_seed='other'),
                              'other': dict(seed_dist=4,
                                            other_dist=2,
                                            other_seed='test'),
                              'wayoff': dict(seed_dist=4,
                                             other_dist=3,
                                             other_seed='test')}
        distances = {}

        conseqs = remap.sam_to_conseqs(sam_file,
                                       seeds=seeds,
                                       original_seeds=seeds,
                                       is_filtered=True,
                                       distance_report=distances)

        self.maxDiff = 1000
        self.assertEqual(expected_conseqs, conseqs)
        self.assertEqual(expected_distances, distances)

开发者ID:cfe-lab，项目名称:MiCall，代码行数:32，代码来源:test_remap.py