def test_correctmapping(self):
runfile = Mock()
d = date(2013, 05, 01)
runfile.date = d
runfile.regions = [1, 2]
runfile.platform = 'Roche454'
r1s1 = mock_sample('Sample1', 'RL1', 'pH1N1', 1, d)
r1s2 = mock_sample('Sample2', 'RL2', 'pH1N1', 1, d)
r2s1 = mock_sample('Sample1', 'RL1', 'pH1N1', 2, d)
r2s2 = mock_sample('Sample2', 'RL2', 'pH1N1', 2, d)
runfile.samples = [r1s1, r1s2, r2s1, r2s2]
result = util.runfile_to_sfffile_mapping(runfile)
mp = fixtures.MIDPREFIX
expect = {
1: {
'454Reads.' + mp + 'RL1.sff':
'Sample1__1__RL1__2013_05_01__pH1N1.sff',
'454Reads.' + mp + 'RL2.sff':
'Sample2__1__RL2__2013_05_01__pH1N1.sff'
},
2: {
'454Reads.' + mp + 'RL1.sff':
'Sample1__2__RL1__2013_05_01__pH1N1.sff',
'454Reads.' + mp + 'RL2.sff':
'Sample2__2__RL2__2013_05_01__pH1N1.sff'
}
}
ere(expect, result)
def test_ensureoutputdir(self):
''' Make sure output dir is created if it doesn't exist '''
outdir = os.path.join(self.tempdir, 'test')
results = demultiplex.demultiplex(self.fp, outdir, self.rf, self.mp,
self.sffc)
common.ere(True, os.path.isdir(outdir))
common.ere(self.rdl, results)
def test_missingfromrunfile( self ):
''' Make sure sff files in the directory that are not in runfile are ignored '''
mock_d = {'1':['454Reads.'+fixtures.MIDPREFIX+'RL1.sff','454Reads.'+fixtures.MIDPREFIX+'IX1.sff']}
self.make_ddir( mock_d )
drds( self.tempdir, fixtures.RUNFILE_PATH )
result = fixtures.mock_demultiplex_directory( self.tempdir )
expect = {1:['Sample1__1__RL1__2013_05_01__pH1N1.sff','454Reads.'+fixtures.MIDPREFIX+'IX1.sff']}
common.ere( expect[1], result[1] )
def test_single_region_single(self):
''' Make sure a single region with single file works '''
mock_d = {'1': ['454Reads.' + fixtures.MIDPREFIX + 'RL1.sff']}
self.make_ddir(mock_d)
drds(self.tempdir, fixtures.RUNFILE_PATH)
expect = {1: ['Sample1__1__RL1__2013_05_01__pH1N1.sff']}
result = fixtures.mock_demultiplex_directory(self.tempdir)
common.ere(expect, result)
def test_multi_region_all_empty(self):
''' Make sure multiple regions that are all empty work '''
mock_d = {'1': [], '2': []}
self.make_ddir(mock_d)
drds(self.tempdir, fixtures.RUNFILE_PATH)
result = fixtures.mock_demultiplex_directory(self.tempdir)
expect = {1: [], 2: []}
common.ere(expect, result)
def test_multi_region_all_empty( self ):
''' Make sure multiple regions that are all empty work '''
mock_d = {'1':[],'2':[]}
self.make_ddir( mock_d )
drds( self.tempdir, fixtures.RUNFILE_PATH )
result = fixtures.mock_demultiplex_directory( self.tempdir )
expect = {1:[],2:[]}
common.ere( expect, result )
def create_and_tst( self, func, sfflist, expectlist, createdir=None ):
''' Create files in sfflist and then test '''
if createdir is None:
createdir = self.tempdir
for f in sfflist:
create( f )
sffs = func( createdir )
ere( expectlist, sffs )
def test_single_region_single( self ):
''' Make sure a single region with single file works '''
mock_d = {'1':['454Reads.'+fixtures.MIDPREFIX+'RL1.sff']}
self.make_ddir( mock_d )
drds( self.tempdir, fixtures.RUNFILE_PATH )
expect = {1:['Sample1__1__RL1__2013_05_01__pH1N1.sff']}
result = fixtures.mock_demultiplex_directory( self.tempdir )
common.ere( expect, result )
def create_and_tst(self, func, sfflist, expectlist, createdir=None):
''' Create files in sfflist and then test '''
if createdir is None:
createdir = self.tempdir
for f in sfflist:
create(f)
sffs = func(createdir)
ere(expectlist, sffs)
def test_multi_region_all_single( self ):
''' Make sure multiple regions that have single files work '''
mp = fixtures.MIDPREFIX
mock_d = {'1':['454Reads.'+mp+'RL1.sff'],'2':['454Reads.'+mp+'TI1.sff']}
self.make_ddir( mock_d )
drds( self.tempdir, fixtures.RUNFILE_PATH )
result = fixtures.mock_demultiplex_directory( self.tempdir )
expect = {1:['Sample1__1__RL1__2013_05_01__pH1N1.sff'],2:['Sample52__2__TI1__2013_05_01__Den4.sff']}
common.ere( expect, result )
def test_getall( self ):
os.mkdir( 'files' )
os.chdir( 'files' )
fs = ('file1.txt','file2.txt')
files = {f:os.path.abspath(f) for f in fs}
# Touch all the files
[open(f,'w').close() for f in files]
ere( sorted(files.values()), sorted(util.get_all_( os.getcwd(), '*.txt' )) )
# Make sure non current dir works
os.chdir( self.tempdir )
ere( sorted(files.values()), sorted(util.get_all_( 'files', '*.txt' )) )
def test_getall(self):
os.mkdir('files')
os.chdir('files')
fs = ('file1.txt', 'file2.txt')
files = {f: os.path.abspath(f) for f in fs}
# Touch all the files
[open(f, 'w').close() for f in files]
ere(sorted(files.values()), sorted(util.get_all_(os.getcwd(),
'*.txt')))
# Make sure non current dir works
os.chdir(self.tempdir)
ere(sorted(files.values()), sorted(util.get_all_('files', '*.txt')))
def test_mixed_files( self ):
''' Make sure all files in root are ignored '''
ddir = 'demultiplex_by_region'
expect = ['454Reads.'+fixtures.MIDPREFIX+'RL1.sff','ignore.me']
os.mkdir( ddir )
os.chdir( ddir )
for f in expect:
common.create( f )
os.chdir( self.tempdir )
drds( ddir, fixtures.RUNFILE_PATH )
result = os.listdir( ddir )
# Just ensure that the files in root didn't change
common.ere( expect, result )
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_mixed_files(self):
''' Make sure all files in root are ignored '''
ddir = 'demultiplex_by_region'
expect = ['454Reads.' + fixtures.MIDPREFIX + 'RL1.sff', 'ignore.me']
os.mkdir(ddir)
os.chdir(ddir)
for f in expect:
common.create(f)
os.chdir(self.tempdir)
drds(ddir, fixtures.RUNFILE_PATH)
result = os.listdir(ddir)
# Just ensure that the files in root didn't change
common.ere(expect, result)
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_multi_region_all_single(self):
''' Make sure multiple regions that have single files work '''
mp = fixtures.MIDPREFIX
mock_d = {
'1': ['454Reads.' + mp + 'RL1.sff'],
'2': ['454Reads.' + mp + 'TI1.sff']
}
self.make_ddir(mock_d)
drds(self.tempdir, fixtures.RUNFILE_PATH)
result = fixtures.mock_demultiplex_directory(self.tempdir)
expect = {
1: ['Sample1__1__RL1__2013_05_01__pH1N1.sff'],
2: ['Sample52__2__TI1__2013_05_01__Den4.sff']
}
common.ere(expect, result)
def test_correctmapping( self ):
runfile = Mock()
d = date( 2013, 05, 01 )
runfile.date = d
runfile.regions = [1,2]
runfile.platform = 'Roche454'
r1s1 = mock_sample( 'Sample1', 'RL1', 'pH1N1', 1, d )
r1s2 = mock_sample( 'Sample2', 'RL2', 'pH1N1', 1, d )
r2s1 = mock_sample( 'Sample1', 'RL1', 'pH1N1', 2, d )
r2s2 = mock_sample( 'Sample2', 'RL2', 'pH1N1', 2, d )
runfile.samples = [r1s1,r1s2,r2s1,r2s2]
result = util.runfile_to_sfffile_mapping( runfile )
mp = fixtures.MIDPREFIX
expect = {1:{'454Reads.'+mp+'RL1.sff':'Sample1__1__RL1__2013_05_01__pH1N1.sff', '454Reads.'+mp+'RL2.sff':'Sample2__1__RL2__2013_05_01__pH1N1.sff'},2:{'454Reads.'+mp+'RL1.sff':'Sample1__2__RL1__2013_05_01__pH1N1.sff', '454Reads.'+mp+'RL2.sff':'Sample2__2__RL2__2013_05_01__pH1N1.sff'}}
ere( expect, result )
def test_missingfromrunfile(self):
''' Make sure sff files in the directory that are not in runfile are ignored '''
mock_d = {
'1': [
'454Reads.' + fixtures.MIDPREFIX + 'RL1.sff',
'454Reads.' + fixtures.MIDPREFIX + 'IX1.sff'
]
}
self.make_ddir(mock_d)
drds(self.tempdir, fixtures.RUNFILE_PATH)
result = fixtures.mock_demultiplex_directory(self.tempdir)
expect = {
1: [
'Sample1__1__RL1__2013_05_01__pH1N1.sff',
'454Reads.' + fixtures.MIDPREFIX + 'IX1.sff'
]
}
common.ere(expect[1], result[1])
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_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_getallblank(self):
ere([], util.get_all_('.', '*'))
open('file', 'w').close()
ere([], util.get_all_('.', '*.txt'))
def test_blanksffnooutput(self):
''' Make sure outputdir is not created if no sff files found '''
outputdir = os.path.join(self.tempdir, 'emptydir')
results = demultiplex.demultiplex(self.tempdir, outputdir, self.rf,
self.mp, self.sffc)
common.ere(False, os.path.isdir(outputdir))
def test_blanksffnooutput( self ):
''' Make sure outputdir is not created if no sff files found '''
outputdir = os.path.join( self.tempdir, 'emptydir' )
results = demultiplex.demultiplex( self.tempdir, outputdir, self.rf, self.mp, self.sffc )
common.ere( False, os.path.isdir( outputdir ) )
def test_getallblank( self ):
ere( [], util.get_all_( '.', '*' ) )
open( 'file','w' ).close()
ere( [], util.get_all_( '.', '*.txt' ) )
def test_ensureoutputdir( self ):
''' Make sure output dir is created if it doesn't exist '''
outdir = os.path.join( self.tempdir, 'test' )
results = demultiplex.demultiplex( self.fp, outdir, self.rf, self.mp, self.sffc )
common.ere( True, os.path.isdir( outdir ) )
common.ere( self.rdl, results )
def test_doesitwork( self ):
lst = ['a1', 'a10', 'a01']
expect = ['a1', 'a01', 'a10']
result = demultiplex.sort_midlist( lst )
common.ere( expect, result )
def pathtest( self, path, t, expect ):
print "Path: {}".format(path)
print "Type: {}".format(t)
result = util.is_valid_abs_path( path, t )
ere( expect, result )
def test_doesitwork(self):
lst = ['a1', 'a10', 'a01']
expect = ['a1', 'a01', 'a10']
result = demultiplex.sort_midlist(lst)
common.ere(expect, result)
def pathtest(self, path, t, expect):
print "Path: {}".format(path)
print "Type: {}".format(t)
result = util.is_valid_abs_path(path, t)
ere(expect, result)
