def test_outputdiraleady( self ):
''' Output directory already created '''
outdir = self.tempdir
results = demultiplex.demultiplex( self.fp, outdir, self.rf, self.mp, self.sffc )
# Get region list
expected_dirs = [str(int(os.path.splitext(n)[0][-2:])) for n in fixtures.multiplex_sffs()]
# Ensure output directory created
common.ere( True, os.path.isdir( outdir ) )
# Ensure region directories
common.ere( expected_dirs, os.listdir( outdir ) )
# Ensure results are correct
common.ere( self.rdl, results )
def test_singleinputsff( self ):
''' Make sure single sff works '''
multiplex_files = fixtures.multiplex_sffs().items()
sfffile = multiplex_files[0][0]
expect = os.path.join( self.tempdir, 'sff', sfffile )
os.mkdir( 'sff' )
# symlink in a fixture sff file
os.symlink( multiplex_files[0][1], expect )
outdir = os.path.join( self.tempdir, 'test' )
results = demultiplex.demultiplex( 'sff', outdir, self.rf, self.mp, self.sffc )
expected_dirs = [str(int(os.path.splitext(expect)[0][-2:]))]
common.ere( expected_dirs, os.listdir( outdir ) )
common.ere( {sfffile:self.rdl[sfffile]}, results )
def test_singleinputsff(self):
''' Make sure single sff works '''
multiplex_files = fixtures.multiplex_sffs().items()
sfffile = multiplex_files[0][0]
expect = os.path.join(self.tempdir, 'sff', sfffile)
os.mkdir('sff')
# symlink in a fixture sff file
os.symlink(multiplex_files[0][1], expect)
outdir = os.path.join(self.tempdir, 'test')
results = demultiplex.demultiplex('sff', outdir, self.rf, self.mp,
self.sffc)
expected_dirs = [str(int(os.path.splitext(expect)[0][-2:]))]
common.ere(expected_dirs, os.listdir(outdir))
common.ere({sfffile: self.rdl[sfffile]}, results)
def test_outputdiraleady(self):
''' Output directory already created '''
outdir = self.tempdir
results = demultiplex.demultiplex(self.fp, outdir, self.rf, self.mp,
self.sffc)
# Get region list
expected_dirs = [
str(int(os.path.splitext(n)[0][-2:]))
for n in fixtures.multiplex_sffs()
]
# Ensure output directory created
common.ere(True, os.path.isdir(outdir))
# Ensure region directories
common.ere(expected_dirs, os.listdir(outdir))
# Ensure results are correct
common.ere(self.rdl, results)
class TestDemultiplexSff(common.BaseClass):
sffs = fixtures.multiplex_sffs()
rf = RunFile(fixtures.RUNFILE_PATH)
expected_read_list = fixtures.demultiplex_reads_lst()
sfffilecmd = which('sfffile')
def setUp(self):
super(TestDemultiplexSff, self).setUp()
def test_ensureabspath(self):
''' sfffile, midparsefile, sfffilecmd and outputdir all need to abspaths '''
try:
demultiplex.demultiplex_sff('sfffile', 'MidParse.conf', ['Mid1'],
'sfffilecmd', 'outputdir')
assert False, 'Should have raised exception as there is a non abspath'
except ValueError as e:
assert True
def test_outputdir_notexist(self):
''' Make sure outputdir gets created if it doesn't exist '''
sffn, sffp = self.sffs.items()[0]
try:
demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE, ['Mid1'],
self.sfffilecmd, 'outputdir')
assert True
except OSError as e:
assert False, 'Output dir didn\'t exist and threw an error which is incorrect'
def test_emptymidlist(self):
''' Empty midlist should raise exception '''
try:
demultiplex.demultiplex_sff('', '', [], '', '')
assert False, 'Empty midlist did not raise exception'
except ValueError as e:
assert True
def test_midlist_missing(self):
sffn, sffp = self.sffs.items()[0]
reg = int(sffn.replace('.sff', '')[-2:])
process = demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE,
self.rf[reg].keys() + ['RL99'],
self.sfffilecmd, self.tempdir)
stdout, stderr = process.communicate()
read_lst = self.expected_read_list[sffn.replace('.sff', '.lst')]
with open(read_lst) as fh:
result = fh.read(
) + ' ' + fixtures.MIDPREFIX + 'RL99: 0 reads found\n'
common.erdiff(result, stdout)
def test_midlist_missingrev(self):
''' Make sure only midkey list barcodes are extracted '''
sffn, sffp = self.sffs.items()[0]
reg = int(sffn.replace('.sff', '')[-2:])
keys = demultiplex.sort_midlist(self.rf[reg].keys())[:-2]
process = demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE, keys,
self.sfffilecmd, self.tempdir)
stdout, stderr = process.communicate()
read_lst = self.expected_read_list[sffn.replace('.sff', '.lst')]
with open(read_lst) as fh:
expect = "".join(fh.readlines()[:-2])
common.erdiff(expect, stdout)
def test_demultiplex_sff(self):
''' Should match expected output from fixtures '''
for sffn, sffp in self.sffs.items():
reg = int(sffn.replace('.sff', '')[-2:])
read_lst = self.expected_read_list[sffn.replace('.sff', '.lst')]
process = demultiplex.demultiplex_sff(sffp, fixtures.MIDPARSE,
self.rf[reg].keys(),
self.sfffilecmd,
self.tempdir)
stdout, stderr = process.communicate()
with open(read_lst) as fh:
common.erdiff(fh.read(), stdout)