def extract_reads( self, dstdir ):
'''
Extracts all of the read files into dstdir
essentially doubling+uncompressed space the amount of storage
@returns a list of abspaths to the extracted reads
'''
extracted_reads = []
for readgz in self.get_reads():
bn,ext = splitext( basename(readgz) )
read = join(dstdir,bn)
util.ungzip( readgz, read )
extracted_reads.append( read )
return extracted_reads
def test_optionalthird(self):
''' Test that given a correct third argument it still runs '''
infa = ungzip(INPUT_PATH)
bwa.index_ref(REF_PATH)
# I don't have a mates file so just use infa again
mem = BWAMem(REF_PATH, infa, infa, bwa_path=BWA_PATH)
eq_(0, mem.run())
def test_optionalthird( self ):
''' Test that given a correct third argument it still runs '''
infa = ungzip( INPUT_PATH )
bwa.index_ref( REF_PATH )
# I don't have a mates file so just use infa again
mem = BWAMem( REF_PATH, infa, infa, bwa_path=BWA_PATH )
eq_( 0, mem.run() )
def setUpClass( self ):
super( SeqIOBase, self ).setUpClass()
self.sff_input = os.path.join( self.tempdir, 'input.sff' )
util.ungzip( util.INPUT_SFF_PATH, self.sff_input )
def test_bwamem_run( self ):
''' Make sure it actually runs bwa with correct input '''
infa = ungzip( INPUT_PATH )
bwa.index_ref( REF_PATH )
mem = BWAMem( REF_PATH, infa, bwa_path=BWA_PATH )
eq_( 0, mem.run() )
def setUpClass(self):
super(SeqIOBase, self).setUpClass()
self.sff_input = os.path.join(self.tempdir, 'input.sff')
util.ungzip(util.INPUT_SFF_PATH, self.sff_input)