def test_error_barcodes(self):
a = BarcodeAssigner([], mismatches=1)
obs = a._error_barcodes("AGG")
exp = [
"CGG", "GGG", "TGG",
"AAG", "ACG", "ATG",
"AGA", "AGC", "AGT",
]
self.assertEqual(set(obs), set(exp))
def test_error_barcodes(self):
a = BarcodeAssigner([], mismatches=1)
obs = a._error_barcodes("AGG")
exp = [
"CGG", "GGG", "TGG",
"AAG", "ACG", "ATG",
"AGA", "AGC", "AGT",
]
self.assertEqual(set(obs), set(exp))
def test_one_mismatch(self):
s = MockSample("Abc", "ACCTGAC")
a = BarcodeAssigner([s], mismatches=1, revcomp=True)
self.assertEqual(a.read_counts, {"Abc": 0})
# 0 mismatches
self.assertEqual(a.assign("GTCAGGT"), s)
self.assertEqual(a.read_counts, {"Abc": 1})
# 1 mismatch
self.assertEqual(a.assign("GTCAAGT"), s)
self.assertEqual(a.read_counts, {"Abc": 2})
# 2 mismatches
self.assertEqual(a.assign("GTCAAAT"), None)
self.assertEqual(a.read_counts, {"Abc": 2})
def test_one_mismatch(self):
s = MockSample("Abc", "ACCTGAC")
a = BarcodeAssigner([s], mismatches=1, revcomp=True)
self.assertEqual(a.read_counts, {"Abc": 0, 'unassigned': 0})
# 0 mismatches
self.assertEqual(a.assign("GTCAGGT"), s)
self.assertEqual(a.read_counts, {"Abc": 1, 'unassigned': 0})
# 1 mismatch
self.assertEqual(a.assign("GTCAAGT"), s)
self.assertEqual(a.read_counts, {"Abc": 2, 'unassigned': 0})
# 2 mismatches
self.assertEqual(a.assign("GTCAAAT"), None)
self.assertEqual(a.read_counts, {"Abc": 2, 'unassigned': 1})
def test_demultiplex(self):
idx = StringIO("@a\nACGTACGT\n+\n9812734[\n"
"@b\nGGGGCGCT\n+\n78154987\n"
"@c\nCCTTCCTT\n+\nkjafd;;;\n")
fwd = StringIO("@a\nGACTGCAGACGACTACGACGT\n+\n8A7T4C2G3CkAjThCeArG;\n"
"@b\nCAGTCAGACGCGCATCAGATC\n+\n78154987bjhasf78612rb\n"
"@c\nTCAGTACGTACGATACGTACG\n+\nkjafd;;;hjfasd82AHG99\n")
rev = StringIO("@a\nCATACGACGACTACGACTCAG\n+\nkjfhda987123GA;,.;,..\n"
"@b\nGTNNNNNNNNNNNNNNNNNNN\n+\n#####################\n"
"@c\nACTAGACTACGCATCAGCATG\n+\nkjafd;;;hjfasd82AHG99\n")
x = IndexFastqSequenceFile(fwd, rev, idx)
w = MockWriter()
# Barcode has 0 mismatches with second index read
s1 = MockSample("SampleS1", "GGGGCGCT")
a = BarcodeAssigner([s1], mismatches=0, revcomp=False)
x.demultiplex(a, w)
# One read was written to SampleS1
self.assertEqual(len(w.written["SampleS1"]), 1)
# That read was the second of three above
r1, r2 = w.written["SampleS1"][0]
self.assertEqual(r1.desc, "b")
self.assertEqual(r1.seq, "CAGTCAGACGCGCATCAGATC")
self.assertEqual(r1.qual, "78154987bjhasf78612rb")
self.assertEqual(r2.desc, "b")
self.assertEqual(r2.seq, "GTNNNNNNNNNNNNNNNNNNN")
self.assertEqual(r2.qual, "#####################")
def test_demultiplex(self):
x = NoIndexFastqSequenceFile(
open(os.path.join(DATA_DIR, "med_R1.fastq")),
open(os.path.join(DATA_DIR, "med_R2.fastq")))
w = MockWriter()
# Barcode matches the 4th read
s1 = MockSample("SampleS1", "GTTTCGCCCTAGTACA")
a = BarcodeAssigner([s1], mismatches=0, revcomp=False)
x.demultiplex(a, w)
# One read was written to SampleS1
self.assertEqual(len(w.written["SampleS1"]), 1)
obs_fwd_read, obs_rev_read = w.written["SampleS1"][0]
# That read was the 4th read
with open(os.path.join(DATA_DIR, "med_R1.fastq")) as f:
expected_fwd_read = list(parse_fastq(f))[3]
self.assertEqual(obs_fwd_read.as_tuple(), expected_fwd_read)
with open(os.path.join(DATA_DIR, "med_R2.fastq")) as f:
expected_rev_read = list(parse_fastq(f))[3]
self.assertEqual(obs_rev_read.as_tuple(), expected_rev_read)
def test_demultiplex(self):
idx = open(os.path.join(DATA_DIR, "tiny_I1.fastq"))
fwd = open(os.path.join(DATA_DIR, "tiny_R1.fastq"))
rev = open(os.path.join(DATA_DIR, "tiny_R2.fastq"))
x = IndexFastqSequenceFile(fwd, rev, idx)
w = MockWriter()
# Barcode has 0 mismatches with second index read
s1 = MockSample("SampleS1", "GGGGCGCT")
a = BarcodeAssigner([s1], mismatches=0, revcomp=False)
x.demultiplex(a, w)
# One read was written to SampleS1
self.assertEqual(len(w.written["SampleS1"]), 1)
# That read was the second of three above
r1, r2 = w.written["SampleS1"][0]
self.assertEqual(r1.desc, "b")
self.assertEqual(r1.seq, "CAGTCAGACGCGCATCAGATC")
self.assertEqual(r1.qual, "78154987bjhasf78612rb")
self.assertEqual(r2.desc, "b")
self.assertEqual(r2.seq, "GTNNNNNNNNNNNNNNNNNNN")
self.assertEqual(r2.qual, "#####################")
def test_demultiplex(self):
fwd = StringIO(fastq_with_barcode_fwd)
rev = StringIO(fastq_with_barcode_rev)
x = NoIndexFastqSequenceFile(fwd, rev)
w = MockWriter()
# Barcode matches the 4th read
s1 = MockSample("SampleS1", "GTTTCGCCCTAGTACA")
a = BarcodeAssigner([s1], mismatches=0, revcomp=False)
x.demultiplex(a, w)
# One read was written to SampleS1
self.assertEqual(len(w.written["SampleS1"]), 1)
# That read was the 4th read
r1, r2 = w.written["SampleS1"][0]
self.assertEqual(
r1.desc,
"HWI-D00727:9:C6JHHANXX:8:1101:1786:2183 1:N:0:GTTTCGCCCTAGTACA")
self.assertEqual(
r1.seq,
"ACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA"
"AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAACCATCAC")
self.assertEqual(
r1.qual,
"A3BBBDGGDEFBGBGG@F@FGEGGGGGGGGGGGGGGGEGGGDGBGBGBEFGCDG>GGGGGG1B"
"FGGG1<FGGGGGGFGG0B>>F0FGGGGC/BBGGECF0@DGD@ADB000;=FGGGGBEBB/@@G")
self.assertEqual(
r2.desc,
"HWI-D00727:9:C6JHHANXX:8:1101:1786:2183 2:N:0:GTTTCGCCCTAGTACA")
self.assertEqual(
r2.seq,
"CATCTTACGCTGCCGACGATCTACTCTTTAGAAATGTCGTTCGTTTTGACTTCTGTAGAATAA"
"GAATGTACTGCTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAG")
self.assertEqual(
r2.qual,
"33:A?11;@/;/;0//////001>11>111111111?10:E0=/1:/1/1111111=11111>"
"11?:=FDEGBGGGG/EB<==@DDFGBEGC00C:>>D.FCG<CDGGGBGGBGGE=E..DGGE/C")