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)))
