Exemple #1
0
 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 ) )
Exemple #2
0
 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')