Example #1
0
    def testGetRestOfPaths(self):
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr19   11   .       ACT     A       20      PASS    .       GT      1/1\n
chr19   15   .       ACGATT      AA       20       PASS    .      GT      1/1\n
chr19   16   .       ACG      A        20      PASS    .       GT      1/1\n
chr19   22   .       ATT       A         20      PASS    .       GT      0/1\n
"""
        pred_io = StringIO.StringIO(pred_str)
        pred_vcf = vcf.Reader(pred_io)
        pred_vars = Variants(pred_vcf,MAX_INDEL_LEN)
        viw = extract_range_and_filter(pred_vars.on_chrom('chr19'),10,25,11)

        paths = _getRestOfPath([], _getOverlaps([],viw))
        #all paths take variants at pos 11 and 22; one takes pos 15, one pos 16
        self.assertEqual(len(paths),2)
        self.assertEqual(len(paths[0]),3)
        self.assertEqual(len(paths[1]),3)
        self.assertTrue(all(map(lambda e: any(map(lambda x: x.pos == 11, e)), paths)))
        self.assertTrue(all(map(lambda e: any(map(lambda x: x.pos == 22, e)), paths)))
        self.assertTrue(any(map(lambda x: x.pos == 15, paths[0])))
        self.assertFalse(any(map(lambda x: x.pos == 16, paths[0])))
        self.assertFalse(any(map(lambda x: x.pos == 15, paths[1])))
        self.assertTrue(any(map(lambda x: x.pos == 16, paths[1])))
Example #2
0
    def testGetOverlaps(self):
        pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
chr19   10   .       ACT     A       20      PASS    .       GT      1/1\n
chr19   13   .       AC      A       20       PASS    .      GT      1/1\n
chr19   14   .       TAGG      TA        20      PASS    .       GT      1/1\n
chr19   15   .       AGG       A         20      PASS    .       GT      0/1\n
chr19   19  .       T       TAAAC 20      PASS    .       GT      0/1
"""
        pred_io = StringIO.StringIO(pred_str)
        pred_vcf = vcf.Reader(pred_io)
        pred_vars = Variants(pred_vcf,MAX_INDEL_LEN)
        variants_in_window = extract_range_and_filter(pred_vars.on_chrom('chr19'),10,20,10)

        #the three overlapping variants should be in same group
        overlaps = _getOverlaps([], variants_in_window)
        self.assertEqual(len(overlaps),3)
        self.assertEqual(map(lambda o: len(o),overlaps),[1,3,1])