def test_filter_alignment(self):
bowtie2Wrap.filter_alignment(self.targetAlignFile, self.filterAlignFiles,
self.outAlignFile)
expectedReadId = ["HWI-ST998R:270:H7NJ9ADXX:1:1101:1797:1927:A"]
with open(self.outAlignFile,'r') as in1:
count = 0
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
continue
l = ln.split('\t')
readId=l[0]
self.assertTrue(count < len(expectedReadId),
"Filter Alignment: Expected number of reads Mismatch!")
self.assertTrue(readId == expectedReadId[count],
"Filter Alignment: Expected Reads Mismatch!")
count += 1
self.assertTrue(count == len(expectedReadId),
"Filter Alignment: Expected number of reads Mismatch!")
def test_filter_alignment(self):
bowtie2Wrap.filter_alignment(self.targetAlignFile,
self.filterAlignFiles, self.outAlignFile)
expectedReadId = ["HWI-ST998R:270:H7NJ9ADXX:1:1101:1797:1927:A"]
with open(self.outAlignFile, 'r') as in1:
count = 0
for ln in in1:
if (ln[0] == '@' or ln[0] == '#'):
continue
l = ln.split('\t')
readId = l[0]
self.assertTrue(
count < len(expectedReadId),
"Filter Alignment: Expected number of reads Mismatch!")
self.assertTrue(readId == expectedReadId[count],
"Filter Alignment: Expected Reads Mismatch!")
count += 1
self.assertTrue(
count == len(expectedReadId),
"Filter Alignment: Expected number of reads Mismatch!")
def filter_alignment(targetAlignFile, filterAlignFiles, outAlignFile):
return bowtie2Wrap.filter_alignment(targetAlignFile, filterAlignFiles,
outAlignFile)
def filter_alignment(targetAlignFile, filterAlignFiles, outAlignFile): return bowtie2Wrap.filter_alignment(targetAlignFile, filterAlignFiles, outAlignFile)
