def test_linkreadsbysample_multidir( self ):
''' Make sure a directory with directories containing reads works '''
structure.create_directory_structure()
plat = self.platforms[0]
platd = os.path.join( self.readdatadir, plat )
ddir = os.path.join( platd, 'demultiplexed' )
os.chdir( platd )
# Make some fake region dirs
os.makedirs( os.path.join( ddir, '1' ) )
os.makedirs( os.path.join( ddir, '2' ) )
rfs = ('sample_1.ab1','sample_1.sff','sample_1.fastq','sample_2.fastq','readme.txt')
fake_samples = {'1':rfs,'2':rfs}
# Populate fake regions
for reg, samples in fake_samples.items():
for sample in samples:
common.create( os.path.join( ddir, reg, reg+sample ) )
print os.listdir( os.path.join( ddir, reg ) )
structure.link_reads_by_sample( ddir, self.readsbysampledir )
os.chdir( self.readsbysampledir )
for reg, samples in fake_samples.items():
print os.listdir( self.readsbysampledir )
for sample in samples:
if 'readme.txt' in sample:
continue
dname, ext = os.path.splitext( sample )
assert os.path.isdir( reg+dname ), "Read directory {} doesn't exist".format(reg+dname)
def make_ddir(self, sffs):
''' Create mock directory from dictionary '''
for rdir, sffs in sffs.items():
os.mkdir(rdir)
os.chdir(rdir)
for sff in sffs:
common.create(sff)
os.chdir('../')
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 make_ddir( self, sffs ):
''' Create mock directory from dictionary '''
for rdir, sffs in sffs.items():
os.mkdir( rdir )
os.chdir( rdir )
for sff in sffs:
common.create( sff )
os.chdir( '../' )
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_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_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_lrbs( self ):
''' Make sure that any list of valid reads get linked '''
structure.create_directory_structure()
rfs = ('sample_1.ab1','sample_1.sff','sample_1.fastq','sample_2.fastq','readme.txt')
expected_dirs = {'sample_1': ['sample_1.ab1','sample_1.fastq','sample_1.sff'], 'sample_2':['sample_2.fastq']}
outpaths = []
# Touch all the read filenames inside of each platform
for plat in self.platforms:
for read in rfs:
rpath = os.path.join( self.readdatadir, plat, read )
outpaths.append( rpath )
common.create( rpath )
# This should link all of the outpaths into the readsbysampledir
platpath = os.path.join( self.readdatadir, plat )
structure.link_reads_by_sample( platpath, self.readsbysampledir )
print "Paths touched: {}".format(outpaths)
# Now there should be directories for each read
sampledirs = os.listdir( self.readsbysampledir )
eq_( sorted(expected_dirs.keys()), sorted(sampledirs) )
for sample,expectedfiles in expected_dirs.items():
resultfiles = os.listdir( os.path.join( self.readsbysampledir, sample ) )
eq_( sorted( expectedfiles ), sorted( resultfiles ) )