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{0}.fa'.format(reads) util.create_fakefasta(filename, reads) print "Reads In File: {0}".format(reads) print "Read Lines: {0}".format(testline) bwa = BWAMem(self.fa, filename, bwa_path=BWA_PATH) eq_(0, bwa.bwa_return_code(testline))
def test_bwareturncode_noendline(self): bwa = BWAMem(self.fa, self.fa2, bwa_path=BWA_PATH) eq_(1, bwa.bwa_return_code('[main] Version: 0.7.4-r385'))
def test_bwareturncode_nocount(self): ''' Make sure if no read sequences lines exist error is returned ''' endline = '[main] Version: {0}.{1}.{2}-r{3}' bwa = BWAMem(self.fa, self.fa2, bwa_path=BWA_PATH) eq_(1, bwa.bwa_return_code(endline.format(0, 7, 4, 385)))