def test_bwareturncode_count( self ):
''' Fixed tests for pattern matching '''
# First item should be the sum of read counts
tests = [
(1, '[M::main_mem] read 1 sequences (111350 bp)...'),
(1000, '[M::main_mem] read 100 sequences (111350 bp)...\n[M::main_mem] read 900 sequences (111350 bp)...'),
]
for reads, testline in tests:
filename = 'fasta{}.fa'.format(reads)
util.create_fakefasta( filename, reads )
print "Reads In File: {}".format(reads)
print "Read Lines: {}".format(testline)
bwa = BWAMem( self.fa, filename, bwa_path=BWA_PATH )
eq_( 0, bwa.bwa_return_code( testline ) )
def setUp(self):
self.t = tempfile.mkdtemp(prefix='isindex')
os.chdir(self.t)
self.fake_ref = util.create_fakefasta('ref.fa', 1)
self.index_ext = ('amb', 'ann', 'bwt', 'pac', 'sa')