def test_load(self):
def compare(read, values):
assert read.qname == values[0]
assert read.flag == values[1]
assert read.ref == values[2]
assert read.pos == values[3]
assert read.mapq == values[4]
assert np.array_equal(read.cigar, values[5])
assert read.rnext == values[6]
assert read.pnext == values[7]
assert read.tlen == values[8]
assert read.seq == values[9]
assert read.qual == values[10]
assert len(read.tags) == values[11]
assert read.strand == values[12]
reads = Reads()
reads.load(self.sam1_file)
compare(reads[0], [
'SRR038105.1', 0, 'chrXI', 128390, 35, [(0, 15)], -1, -1, 0,
'GATATGATGGATTTG', 'FDFFFFFFFFFFFCF', 9, 1
])
# SRR038105.1000167 0 chrXIV 703158 42 15M * 0 0 TACGGTATTGGTCGG FFFFCFFFFFFFFCF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
res = reads.get_read_by_qname('SRR038105.1000167')
compare(res, [
'SRR038105.1000167', 0, 'chrXIV', 703158, 42, [(0, 15)], -1, -1, 0,
'TACGGTATTGGTCGG', 'FFFFCFFFFFFFFCF', 8, 1
])
# SRR038105.1000320 0 chrXVI 577162 35 15M * 0 0 TTGATAAAATAGTCC <<@FF<FFFFAFAFA AS:i:0 XS:i:-5 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
res = reads.get_read_by_qname('SRR038105.1000320')
compare(res, [
'SRR038105.1000320', 0, 'chrXVI', 577162, 35, [(0, 15)], -1, -1, 0,
'TTGATAAAATAGTCC', '<<@FF<FFFFAFAFA', 9, 1
])
# check unpaired right
# SRR038105.1000002 16 chrIV 203242 42 16M * 0 0 ACCCATTATTTCTCGA IIIIIFIICIFIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
res = reads.get_read_by_qname('SRR038105.1000002')
assert res is None
# check unpaired left
# SRR038105.1000011 16 chrIV 526796 42 16M * 0 0 GGTGAATTAGAAGATA FFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
res = reads.get_read_by_qname('SRR038105.1000011')
compare(res, [
'SRR038105.1000011', 16, 'chrIV', 526796, 42, [(0, 16)], -1, -1, 0,
'GGTGAATTAGAAGATA', 'FFFFFFFFFFFFFFFF', 8, -1
])
reads.close()
class TestBWAFragmentMappedReads:
def setup_method(self, method):
self.dir = os.path.dirname(os.path.realpath(__file__))
sam1_file = self.dir + "/test_seq/test_bwa1.sam"
sam2_file = self.dir + "/test_seq/test_bwa2.sam"
self.reads1 = Reads()
self.reads2 = Reads()
self.reads1.load(sam1_file)
self.reads2.load(sam2_file)
self.reads1.filter_unmapped()
self.reads2.filter_unmapped()
self.genome = Genome.from_folder(self.dir + "/test_seq/dmel_genome/")
self.pairs = FragmentMappedReadPairs()
regions = self.genome.get_regions('MboI')
self.pairs.load(self.reads1, self.reads2, regions=regions)
regions.close()
def teardown_method(self, method):
self.reads1.close()
self.reads2.close()
self.genome.close()
self.pairs.close()
def test_loaded_bwamem_pairs(self):
assert self.pairs._single_count == 896
assert self.pairs._pair_count == 515
def test_pcr_duplicate_filter(self):
mask = self.pairs.add_mask_description(
'pcr_duplicate', 'Mask suspected PCR duplicates.')
pcr_duplicate_filter = PCRDuplicateFilter(pairs=self.pairs,
threshold=3)
assert len(self.pairs) == 515
self.pairs.filter(pcr_duplicate_filter)
assert len(self.pairs) == 512
def test_build_from_scratch(self):
reads = Reads()
reads.load(self.sam1_file)
assert len(reads) == 271
reads.close()
