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()
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()
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()
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()