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)