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')