示例#1
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    def test_tophat_paired(self):
        reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
        reads_1_fpath = os.path.join(TEST_DATA_DIR, 'reads_1.fastq')
        reads_2_fpath = os.path.join(TEST_DATA_DIR, 'reads_2.fastq')
        try:
            directory = TemporaryDir()
            index_fpath = get_or_create_bowtie2_index(reference_fpath,
                                                      directory.name)
            map_with_tophat(index_fpath, directory.name,
                            paired_fpaths=[reads_1_fpath, reads_2_fpath])
            os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
            self.fail('runtimeError expected')
        except RuntimeError:
            pass
        finally:
            directory.close()

        try:
            directory = TemporaryDir()
            index_fpath = get_or_create_bowtie2_index(reference_fpath,
                                                      directory.name)
            map_with_tophat(index_fpath, directory.name,
                            paired_fpaths=[reads_1_fpath, reads_2_fpath],
                            mate_inner_dist=350, mate_std_dev=50)
            os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
        finally:
            directory.close()
示例#2
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    def test_tophat_paired(self):
        reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
        reads_1_fpath = os.path.join(TEST_DATA_DIR, 'reads_1.fastq')
        reads_2_fpath = os.path.join(TEST_DATA_DIR, 'reads_2.fastq')
        try:
            directory = TemporaryDir()
            index_fpath = get_or_create_bowtie2_index(reference_fpath,
                                                      directory.name)
            map_with_tophat(index_fpath,
                            directory.name,
                            paired_fpaths=[reads_1_fpath, reads_2_fpath])
            os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
            self.fail('runtimeError expected')
        except RuntimeError:
            pass
        finally:
            directory.close()

        try:
            directory = TemporaryDir()
            index_fpath = get_or_create_bowtie2_index(reference_fpath,
                                                      directory.name)
            map_with_tophat(index_fpath,
                            directory.name,
                            paired_fpaths=[reads_1_fpath, reads_2_fpath],
                            mate_inner_dist=350,
                            mate_std_dev=50)
            os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
        finally:
            directory.close()
示例#3
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 def test_tophat(self):
     reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
     reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
     directory = TemporaryDir()
     index_fpath = get_or_create_bowtie2_index(reference_fpath,
                                               directory.name)
     map_with_tophat(index_fpath, directory.name,
                     unpaired_fpath=reads_fpath)
     os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
     directory.close()
示例#4
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 def test_tophat(self):
     reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
     reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
     directory = TemporaryDir()
     index_fpath = get_or_create_bowtie2_index(reference_fpath,
                                               directory.name)
     map_with_tophat(index_fpath,
                     directory.name,
                     unpaired_fpath=reads_fpath)
     os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
     directory.close()