Python bowtie2_build_index Examples

Example #1

File: _mapper_test.py Project: shaharazulay/unicorn

    def test_missing_inputs(self):
        magellan.bowtie2_build_index(
            os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
            os.path.join(_sample_data_dir, 'test_index'))

        with self.assertRaises(RuntimeError):
            magellan.bowtie2_map(
                os.path.join(_sample_data_dir, 'madeup.fastq'),
                os.path.join(_sample_data_dir, 'test_index'),
                os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
                os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))

        with self.assertRaises(RuntimeError):
            magellan.bowtie2_map(
                os.path.join(_sample_data_dir,
                             'sample_reads_for_mapper.fastq'),
                os.path.join(_sample_data_dir, 'madeup_index'),
                os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
                os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))

        index_files = glob.glob(os.path.join(_sample_data_dir, 'test_index.*'))
        for i in index_files:
            os.remove(i)

        s = os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam')
        if os.path.isfile(s):
            os.remove(s)
        l = os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam')
        if os.path.isfile(l):
            os.remove(l)

Example #2

File: _mapper_test.py Project: shaharazulay/unicorn

    def setUpClass(cls):

        magellan.bowtie2_build_index(
            os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
            os.path.join(_sample_data_dir, 'test_index'))

        magellan.bowtie2_map(
            os.path.join(_sample_data_dir, 'sample_reads_for_mapper.fastq'),
            os.path.join(_sample_data_dir, 'test_index'),
            os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
            os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))

Example #3

File: _mapper_test.py Project: shaharazulay/unicorn

    def test_basic(self):
        magellan.bowtie2_build_index(
            os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
            os.path.join(_sample_data_dir, 'test_index'))

        index_files = glob.glob(os.path.join(_sample_data_dir, 'test_index.*'))
        for i in index_files:
            os.remove(i)

        magellan.bowtie2_build_index(os.path.join(
            _sample_data_dir, 'sample_bac_genome_short.fa'),
                                     os.path.join(_sample_data_dir,
                                                  'test_index_offrate'),
                                     offrate=2)

        offrate_index_files = glob.glob(
            os.path.join(_sample_data_dir, 'test_index_offrate.*'))
        for i in offrate_index_files:
            os.remove(i)

Example #4

File: _mapper_test.py Project: shaharazulay/unicorn

    def test_basic(self):
        magellan.bowtie2_build_index(
            os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
            os.path.join(_sample_data_dir, 'test_index'))

        magellan.bowtie2_map(
            os.path.join(_sample_data_dir, 'sample_reads_for_mapper.fastq'),
            os.path.join(_sample_data_dir, 'test_index'),
            os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
            os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))

        index_files = glob.glob(os.path.join(_sample_data_dir, 'test_index'))

        for i in index_files:
            os.remove(i)

        os.remove(os.path.join(_sample_data_dir,
                               'sample_reads_for_mapper.sam'))
        os.remove(os.path.join(_sample_data_dir,
                               'sample_reads_for_mapper.log'))

Example #5

File: _mapper_test.py Project: shaharazulay/unicorn

 def test_missing_fasta(self):
     with self.assertRaises(RuntimeError):
         magellan.bowtie2_build_index(
             os.path.join(_sample_data_dir, 'madeup.fa'),
             os.path.join(_sample_data_dir, 'test_index'))