def setUp(self):
# Make test directories
self.empty_dir1 = TestUtils.make_dir()
self.empty_dir2 = TestUtils.make_dir()
self.dir1 = ExampleDirScooby()
self.dir2 = ExampleDirScooby()
self.dir1.create_directory()
self.dir2.create_directory()
def setUp(self):
# Make test directories
self.empty_dir1 = TestUtils.make_dir()
self.empty_dir2 = TestUtils.make_dir()
self.dir1 = ExampleDirScooby()
self.dir2 = ExampleDirScooby()
self.dir1.create_directory()
self.dir2.create_directory()
def setUp(self):
# Make an example directory with sample files
# structured as for SOLiD data
self.d = TestUtils.make_dir()
# Add files
for f in SOLID_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.d)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d,'qc')
for f in SOLID_QC_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.qc_dir)
def setUp(self):
# Make an example directory with sample files
# structured as for SOLiD data
self.d = TestUtils.make_dir()
# Add files
for f in SOLID_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.d)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d, 'qc')
for f in SOLID_QC_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.qc_dir)
def setUp(self):
# Make an example directory with sample files
# structured as for Illumina data
self.d = TestUtils.make_dir()
# Add fastq files
self.fastq_dir = TestUtils.make_sub_dir(self.d,'fastqs')
for f in ILLUMINA_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.fastq_dir)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d,'qc')
for f in ILLUMINA_QC_FILES.split():
TestUtils.make_file(f,"lorem ipsum",basedir=self.qc_dir)
for d in ILLUMINA_FASTQC_DIRS.split():
TestUtils.make_sub_dir(self.qc_dir,d)
def setUp(self):
# Make an example directory with sample files
# structured as for Illumina data
self.d = TestUtils.make_dir()
# Add fastq files
self.fastq_dir = TestUtils.make_sub_dir(self.d, 'fastqs')
for f in ILLUMINA_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.fastq_dir)
# Make an example QC dir
self.qc_dir = TestUtils.make_sub_dir(self.d, 'qc')
for f in ILLUMINA_QC_FILES.split():
TestUtils.make_file(f, "lorem ipsum", basedir=self.qc_dir)
for d in ILLUMINA_FASTQC_DIRS.split():
TestUtils.make_sub_dir(self.qc_dir, d)
def setUp(self):
# Create working directory for test files etc
self.wd = TestUtils.make_dir()
