def setUp(self):
self.fq_for = fake_fh(
'''@MISEQ578:1:1101:17145:1691#TTCAGA/1\nNTCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATCAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAACAACTGTAAGAACTG\n+MISEQ578:1:1101:17145:1691#TTCAGA/1\nB]]P]Pab_cePRPPP`efdde`efeRfgeeRPeeeeb`fffgfadfaeefeeedeabfeddbddfggggfcgfbddeggeggfggeggaeeegggggfgdgggfggeaeaddcfgedePdaddPdffeefeaPPeeefPffgeedaecb[^bfggdbedbggPac^Nb^_gfaMLLb`facgeegeafe[bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:18716:1699#CCTGAG/1\nNCAGCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGGTAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGTTTTTGAGATGGCAGCAACGGAAACCATAACGAGCATCATCTTAGATCGGAAGAGAGGT\n+MISEQ578:1:1101:18716:1699#CCTGAG/1\nBPPP]P]]PbRRcPabffffefefedaPffbPeeegggeggggegfegecfefffffgggacedggggggfgggfffgggggggggfgggggfgfgdgeggggggegdeecffdgafefggegfgQefgeafegeaPeggdfffg`edcga_b^aePfgggfggefeaeOPNNNe[N]LL_LefgeacccaOO\ON[LM[fbbNbb`bMYMZLZMLXMXOZZNXM`__eeaaOOZOXZbBBBBBBBBBBBB\n@MISEQ578:1:1101:16445:1701#CCTGAG/1\nNCGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGACAAATATCAACCACACCAGAAGCAGCATCAGTGACGA\n+MISEQ578:1:1101:16445:1701#CCTGAG/1\nBPPP]]PPPPa_RRaPecPefaPeOdO`eRdfeaeaab`dfeeecePP`dd`eddefPfaea^NeggggeafdeefPPPeddefefadebfegefggeded``_d`efggggggggeaddd`dggggfeeeePaOecefPPeeeabegPeggeafeefeefdffbfeggedaP[PePP]ecOO\cO\ccM[LLLYMbMYYOOZbfbegefeeOXXZZNOXaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:12954:1727#AATGTC/1\nNGTGGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATTATTGGGTTTAAAGGGTCCGCAGGCTGTTTGTTAAGTCAGGGGTGAAATCCTACCGCTCAACGGTAGAACTGCCTTTGATACTGGCAAACTTGAGTTATTGTGAAGTAGTTAGAATGTGTAGTGTAGCGGTGAAATGCATAGATATTACACAGAATACCGATTGCGAAAGCAGATTACTAACAATATACTGACGATGAGG\n+MISEQ578:1:1101:12954:1727#AATGTC/1\nBP]PP]P_]aPPP``e^dd^ddfgefebdbbffeggfgffffegggffNdefgggggfdeebceeefgggffffffgggggggegeggggeaedddggggggfggdfffffgedf^fbeggggggggfgffgggeeefggggggggfecfceafaegcef\[\OcgeaObbeegggegfLbbLdefffaeaeefedeaeOOaO`bNZeead^ZXdfeLZL`aaaNXNaXNZNNNNXNXaaaXeBBBBBBBB\n'''
)
self.fq_rev = fake_fh(
'''@MISEQ578:1:1101:17145:1691#TTCAGA/2\nNTCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATCAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAACAACTGTAAGAACTG\n+MISEQ578:1:1101:17145:1691#TTCAGA/2\nB]]P]Pab_cePRPPP`efdde`efeRfgeeRPeeeeb`fffgfadfaeefeeedeabfeddbddfggggfcgfbddeggeggfggeggaeeegggggfgdgggfggeaeaddcfgedePdaddPdffeefeaPPeeefPffgeedaecb[^bfggdbedbggPac^Nb^_gfaMLLb`facgeegeafe[bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:16445:1701#CCTGAG/2\nNCGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGACAAATATCAACCACACCAGAAGCAGCATCAGTGACGA\n+MISEQ578:1:1101:16445:1701#CCTGAG/2\nBPPP]]PPPPa_RRaPecPefaPeOdO`eRdfeaeaab`dfeeecePP`dd`eddefPfaea^NeggggeafdeefPPPeddefefadebfegefggeded``_d`efggggggggeaddd`dggggfeeeePaOecefPPeeeabegPeggeafeefeefdffbfeggedaP[PePP]ecOO\cO\ccM[LLLYMbMYYOOZbfbegefeeOXXZZNOXaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:12954:1727#AATGTC/2\nNGTGGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATTATTGGGTTTAAAGGGTCCGCAGGCTGTTTGTTAAGTCAGGGGTGAAATCCTACCGCTCAACGGTAGAACTGCCTTTGATACTGGCAAACTTGAGTTATTGTGAAGTAGTTAGAATGTGTAGTGTAGCGGTGAAATGCATAGATATTACACAGAATACCGATTGCGAAAGCAGATTACTAACAATATACTGACGATGAGG\n+MISEQ578:1:1101:12954:1727#AATGTC/2\nBP]PP]P_]aPPP``e^dd^ddfgefebdbbffeggfgffffegggffNdefgggggfdeebceeefgggffffffgggggggegeggggeaedddggggggfggdfffffgedf^fbeggggggggfgffgggeeefggggggggfecfceafaegcef\[\OcgeaObbeegggegfLbbLdefffaeaeefedeaeOOaO`bNZeead^ZXdfeLZL`aaaNXNaXNZNNNNXNXaaaXeBBBBBBBB\n'''
)
def test_correct(self):
in_fh = fake_fh(['@foo', 'AAA', '+foo', '###', '@bar', 'CCC', '+bar', '"""', '@baz', 'TTT', '+baz', '$$$', '@poo', 'GGG', '+poo', '==='])
outs = [fake_fh() for x in range(3)]
split_fastq.split_fastq_entries(in_fh, outs)
conts = [out.getvalue() for out in outs]
exp1 = "\n".join(['@foo', 'AAA', '+', '###', '@poo', 'GGG', '+', '===']) + "\n"
exp2 = "\n".join(['@bar', 'CCC', '+', '"""']) + "\n"
exp3 = "\n".join(['@baz', 'TTT', '+', '$$$']) + "\n"
self.assertEqual(conts, [exp1, exp2, exp3])
def setUp(self):
self.good_fastq_content = "@foo\nAAA\n+foo\n!!!\n@bar\nCCC\n+bar\n###"
self.fastq13 = """@lolapolooza:1234#ACGT/1\nAATTAAGTCAAATTTGGCCTGGCCCAGTGTCCAATGTTGT\n+\nABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh\n"""
self.fastq18 = """@lolapolooza:1234#ACGT/1\nAATTAAGTCAAATTTGGCCTGGCCCAGTGTCCAATGTTGT\n+\n"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI\n"""
self.fastq13_fh = fake_fh(self.fastq13 + "\n")
self.fastq13_record = SeqIO.read(self.fastq13_fh, 'fastq')
self.fastq13_fh.seek(0)
self.fastq18_fh = fake_fh(self.fastq18 + "\n")
self.fastq18_record = SeqIO.read(self.fastq18_fh, 'fastq')
self.fastq18_fh.seek(0)
fh = fake_fh('''@lol:1234#ACGT/1\nAAAA\n+\nAh"J\n''')
self.fastq_ambig_record = SeqIO.read(fh, 'fastq')
def setUp(self):
fasta = fake_fh([
'>foo', 'AA', '>bar', 'CC', '>baz', 'AA', '>blag', 'AA', '>flog',
'TT', '>blob', 'TT'
])
minimum_counts = 2
self.derep = derep_fulllength.Dereplicator(fasta, minimum_counts)
def test_correct(self):
table = {
"seq0": {
"donor1": 5,
"donor2": 10
},
"seq1": {
"donor1": 1,
"donor5": 4
},
"seq2": {
"donor4": 1
}
}
abund = {'seq0': 15, 'seq1': 5, 'seq2': 1}
samples = ['donor1', 'donor2', 'donor4', 'donor5']
cont = "\n".join([
'sequence_id\tdonor1\tdonor2\tdonor4\tdonor5', 'seq0\t5\t10\t0\t0',
'seq1\t1\t0\t0\t4', 'seq2\t0\t0\t1\t0'
]) + "\n"
fh = fake_fh()
seq_table.SeqTableWriter.write_table(table, abund, samples, 0, fh)
fh.seek(0)
cont2 = fh.read()
self.assertEqual(cont, cont2)
def test_correct(self):
in_fh = fake_fh([
'@foo', 'AAA', '+foo', '###', '@bar', 'CCC', '+bar', '"""', '@baz',
'TTT', '+baz', '$$$', '@poo', 'GGG', '+poo', '==='
])
outs = [fake_fh() for x in range(3)]
split_fastq.split_fastq_entries(in_fh, outs)
conts = [out.getvalue() for out in outs]
exp1 = "\n".join(
['@foo', 'AAA', '+', '###', '@poo', 'GGG', '+', '===']) + "\n"
exp2 = "\n".join(['@bar', 'CCC', '+', '"""']) + "\n"
exp3 = "\n".join(['@baz', 'TTT', '+', '$$$']) + "\n"
self.assertEqual(conts, [exp1, exp2, exp3])
def test_parse_derep_fasta(self):
'''should make a dictionary of fasta lines'''
fasta = fake_fh(['>seq0;counts=10', 'AAA', '>seq4;counts=23', 'TTT'])
self.assertEqual(index.parse_derep_fasta(fasta), {
'AAA': 'seq0',
'TTT': 'seq4'
})
def test_correct(self):
fasta = fake_fh(['>sample=donor1;1', 'AAA', '>sample=donor1;2', 'AAA', '>sample=donor2;1', 'AAA', '>sample=donor3;1', 'TTT'])
names = {'AAA': 'seqA', 'TTT': 'seqT'}
table = {'seqA': {'donor1': 2, 'donor2': 1}, 'seqT': {'donor3': 1}}
abund = {'seqA': 3, 'seqT': 1}
table2, abund2 = seq_table.SeqTableWriter.fasta_to_abund(fasta, names)
self.assertEqual(table, table2)
self.assertEqual(abund, abund2)
def setUp(self):
self.fastq = fake_fh(
'''@lolapolooza\nTAAAACATCATCATCAT\n+lolapolooza\n"#$%&'()*+,-./012\n'''
)
self.primer = "AAAA"
self.max_primer_diffs = 1
self.primer_remover = util_primer.PrimerRemover(
self.fastq, self.primer, self.max_primer_diffs)
def test_no_barcode(self):
'''should raise error when no barcode in the @ line'''
d = {'ACGT': 'donor1', 'TACA': 'donor2'}
fastq = fake_fh(['@foo#ACGT/1', 'AAA', '+', 'AAA', '@bar_bad_format/1', 'CCC', '+', 'BBB'])
it = map_barcodes.renamed_fastq_records(fastq, d, 1)
# the first entry is OK, but the second should complain
it.next()
self.assertRaises(RuntimeError, it.next)
def test_correct(self):
'''should collect only the matching entries'''
old_fasta = fake_fh([">a", "AAA", ">b", "TTT", ">c", "GGG"])
labels = ["a", "c"]
expected_new_fasta = ">a\nAAA\n>c\nGGG\n"
new_fasta = uc2denovo.matching_fasta_entries(labels, old_fasta)
self.assertEqual([new_fasta[0].id, str(new_fasta[0].seq), new_fasta[1].id, str(new_fasta[1].seq)], ['a', 'AAA', 'c', 'GGG'])
def test_correct(self):
'''should convert Illumina 1.4-1.7 to our mixed format'''
record18 = convert_fastq.convert_record_illumina13_to_18(self.fastq13_record)
fh = fake_fh()
SeqIO.write(record18, fh, 'fastq')
entry18 = fh.getvalue()
self.assertEqual(entry18, self.fastq18)
def setUp(self):
self.barcode_map = {
'AAA': 'sampleA',
'TTT': 'sampleT',
'CCC': 'sampleC'
}
self.fastq = fake_fh([
'@lol#AAA/1', 'CAT', '+', 'aaa', '@hoo#TTT/1', 'CAT', '+', 'aaa',
'@crap#ACT/1', 'CAT', '+', 'aaa'
])
def test_correct(self):
table = {"seq0": {"donor1": 5, "donor2": 10}, "seq1": {"donor1": 1, "donor5": 4}, "seq2": {"donor4": 1}}
abund = {'seq0': 15, 'seq1': 5, 'seq2': 1}
samples = ['donor1', 'donor2', 'donor4', 'donor5']
cont = "\n".join(['sequence_id\tdonor1\tdonor2\tdonor4\tdonor5', 'seq0\t5\t10\t0\t0', 'seq1\t1\t0\t0\t4', 'seq2\t0\t0\t1\t0']) + "\n"
fh = fake_fh()
seq_table.SeqTableWriter.write_table(table, abund, samples, 0, fh)
fh.seek(0)
cont2 = fh.read()
self.assertEqual(cont, cont2)
def test_correct(self):
fasta = fake_fh([
'>sample=donor1;1', 'AAA', '>sample=donor1;2', 'AAA',
'>sample=donor2;1', 'AAA', '>sample=donor3;1', 'TTT'
])
names = {'AAA': 'seqA', 'TTT': 'seqT'}
table = {'seqA': {'donor1': 2, 'donor2': 1}, 'seqT': {'donor3': 1}}
abund = {'seqA': 3, 'seqT': 1}
table2, abund2 = seq_table.SeqTableWriter.fasta_to_abund(fasta, names)
self.assertEqual(table, table2)
self.assertEqual(abund, abund2)
def test_parse_full_fasta(self):
seq_sid = {'AAA': 'seq0', 'TTT': 'seq4'}
fasta = fake_fh([
'>sample=donor1;1', 'AAA', '>sample=donor1;2', 'AAA',
'>sample=donor1;3', 'TTT', '>sample=donorT;1', 'TTT'
])
abund = index.parse_full_fasta(fasta, seq_sid)
self.assertEqual(abund, {
('donor1', 'seq0'): 2,
('donor1', 'seq4'): 1,
('donorT', 'seq4'): 1
})
def test_correct(self):
'''should properly rename samples'''
d = {'ACGT': 'donor1', 'TACA': 'donor2'}
fastq = fake_fh(['@foo#ACGT/1', 'AAA', '+', 'AAA', '@bar#TACA/1', 'CCC', '+', 'BBB'])
it = map_barcodes.renamed_fastq_records(fastq, d, 1)
record = it.next()
self.assertEqual(str(record.seq), 'AAA')
self.assertEqual(record.id, 'sample=donor1;1/1')
record = it.next()
self.assertEqual(str(record.seq), 'CCC')
self.assertEqual(record.id, 'sample=donor2;1/1')
def test_no_barcode(self):
'''should raise error when no barcode in the @ line'''
d = {'ACGT': 'donor1', 'TACA': 'donor2'}
fastq = fake_fh([
'@foo#ACGT/1', 'AAA', '+', 'AAA', '@bar_bad_format/1', 'CCC', '+',
'BBB'
])
it = map_barcodes.renamed_fastq_records(fastq, d, 1)
# the first entry is OK, but the second should complain
it.next()
self.assertRaises(RuntimeError, it.next)
def test_correct(self):
'''should properly rename samples'''
d = {'ACGT': 'donor1', 'TACA': 'donor2'}
fastq = fake_fh([
'@foo#ACGT/1', 'AAA', '+', 'AAA', '@bar#TACA/1', 'CCC', '+', 'BBB'
])
it = map_barcodes.renamed_fastq_records(fastq, d, 1)
record = it.next()
self.assertEqual(str(record.seq), 'AAA')
self.assertEqual(record.id, 'sample=donor1;1/1')
record = it.next()
self.assertEqual(str(record.seq), 'CCC')
self.assertEqual(record.id, 'sample=donor2;1/1')
def test_parse_derep_fasta(self):
'''should make a dictionary of fasta lines'''
fasta = fake_fh(['>seq0;counts=10', 'AAA', '>seq4;counts=23', 'TTT'])
self.assertEqual(index.parse_derep_fasta(fasta), {'AAA': 'seq0', 'TTT': 'seq4'})
def test_correct(self):
fasta = fake_fh(['>sample=donor1;1', 'AAA', '>sample=donor1;2', 'AAA', '>sample=donor2;1', 'AAA', '>sample=donor3;1', 'TTT'])
table = {'AAA': {'donor1': 2, 'donor2': 1}, 'TTT': {'donor3': 1}}
abund = {'AAA': 3, 'TTT': 1}
self.assertEqual(seq_table.fasta_to_table_and_abund(fasta), (table, abund))
def setUp(self):
self.barcode_map = {'AAA': 'sampleA', 'TTT': 'sampleT', 'CCC': 'sampleC'}
self.fastq = fake_fh(['@lol#AAA/1', 'CAT', '+', 'aaa', '@hoo#TTT/1', 'CAT', '+', 'aaa', '@crap#ACT/1', 'CAT', '+', 'aaa'])
def setUp(self):
self.fq_for = fake_fh('''@MISEQ578:1:1101:17145:1691#TTCAGA/1\nNTCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATCAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAACAACTGTAAGAACTG\n+MISEQ578:1:1101:17145:1691#TTCAGA/1\nB]]P]Pab_cePRPPP`efdde`efeRfgeeRPeeeeb`fffgfadfaeefeeedeabfeddbddfggggfcgfbddeggeggfggeggaeeegggggfgdgggfggeaeaddcfgedePdaddPdffeefeaPPeeefPffgeedaecb[^bfggdbedbggPac^Nb^_gfaMLLb`facgeegeafe[bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:18716:1699#CCTGAG/1\nNCAGCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGGTAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGTTTTTGAGATGGCAGCAACGGAAACCATAACGAGCATCATCTTAGATCGGAAGAGAGGT\n+MISEQ578:1:1101:18716:1699#CCTGAG/1\nBPPP]P]]PbRRcPabffffefefedaPffbPeeegggeggggegfegecfefffffgggacedggggggfgggfffgggggggggfgggggfgfgdgeggggggegdeecffdgafefggegfgQefgeafegeaPeggdfffg`edcga_b^aePfgggfggefeaeOPNNNe[N]LL_LefgeacccaOO\ON[LM[fbbNbb`bMYMZLZMLXMXOZZNXM`__eeaaOOZOXZbBBBBBBBBBBBB\n@MISEQ578:1:1101:16445:1701#CCTGAG/1\nNCGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGACAAATATCAACCACACCAGAAGCAGCATCAGTGACGA\n+MISEQ578:1:1101:16445:1701#CCTGAG/1\nBPPP]]PPPPa_RRaPecPefaPeOdO`eRdfeaeaab`dfeeecePP`dd`eddefPfaea^NeggggeafdeefPPPeddefefadebfegefggeded``_d`efggggggggeaddd`dggggfeeeePaOecefPPeeeabegPeggeafeefeefdffbfeggedaP[PePP]ecOO\cO\ccM[LLLYMbMYYOOZbfbegefeeOXXZZNOXaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:12954:1727#AATGTC/1\nNGTGGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATTATTGGGTTTAAAGGGTCCGCAGGCTGTTTGTTAAGTCAGGGGTGAAATCCTACCGCTCAACGGTAGAACTGCCTTTGATACTGGCAAACTTGAGTTATTGTGAAGTAGTTAGAATGTGTAGTGTAGCGGTGAAATGCATAGATATTACACAGAATACCGATTGCGAAAGCAGATTACTAACAATATACTGACGATGAGG\n+MISEQ578:1:1101:12954:1727#AATGTC/1\nBP]PP]P_]aPPP``e^dd^ddfgefebdbbffeggfgffffegggffNdefgggggfdeebceeefgggffffffgggggggegeggggeaedddggggggfggdfffffgedf^fbeggggggggfgffgggeeefggggggggfecfceafaegcef\[\OcgeaObbeegggegfLbbLdefffaeaeefedeaeOOaO`bNZeead^ZXdfeLZL`aaaNXNaXNZNNNNXNXaaaXeBBBBBBBB\n''')
self.fq_rev = fake_fh('''@MISEQ578:1:1101:17145:1691#TTCAGA/2\nNTCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATCAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAACAACTGTAAGAACTG\n+MISEQ578:1:1101:17145:1691#TTCAGA/2\nB]]P]Pab_cePRPPP`efdde`efeRfgeeRPeeeeb`fffgfadfaeefeeedeabfeddbddfggggfcgfbddeggeggfggeggaeeegggggfgdgggfggeaeaddcfgedePdaddPdffeefeaPPeeefPffgeedaecb[^bfggdbedbggPac^Nb^_gfaMLLb`facgeegeafe[bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:16445:1701#CCTGAG/2\nNCGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGACAAATATCAACCACACCAGAAGCAGCATCAGTGACGA\n+MISEQ578:1:1101:16445:1701#CCTGAG/2\nBPPP]]PPPPa_RRaPecPefaPeOdO`eRdfeaeaab`dfeeecePP`dd`eddefPfaea^NeggggeafdeefPPPeddefefadebfegefggeded``_d`efggggggggeaddd`dggggfeeeePaOecefPPeeeabegPeggeafeefeefdffbfeggedaP[PePP]ecOO\cO\ccM[LLLYMbMYYOOZbfbegefeeOXXZZNOXaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@MISEQ578:1:1101:12954:1727#AATGTC/2\nNGTGGTGCCAGCAGCCGCGGTAATACGGAGGATCCAAGCGTTATCCGGAATTATTGGGTTTAAAGGGTCCGCAGGCTGTTTGTTAAGTCAGGGGTGAAATCCTACCGCTCAACGGTAGAACTGCCTTTGATACTGGCAAACTTGAGTTATTGTGAAGTAGTTAGAATGTGTAGTGTAGCGGTGAAATGCATAGATATTACACAGAATACCGATTGCGAAAGCAGATTACTAACAATATACTGACGATGAGG\n+MISEQ578:1:1101:12954:1727#AATGTC/2\nBP]PP]P_]aPPP``e^dd^ddfgefebdbbffeggfgffffegggffNdefgggggfdeebceeefgggffffffgggggggegeggggeaedddggggggfggdfffffgedf^fbeggggggggfgffgggeeefggggggggfecfceafaegcef\[\OcgeaObbeegggegfLbbLdefffaeaeefedeaeOOaO`bNZeead^ZXdfeLZL`aaaNXNaXNZNNNNXNXaaaXeBBBBBBBB\n''')
def setUp(self):
fasta = fake_fh(['>foo', 'AA', '>bar', 'CC', '>baz', 'AA', '>blag', 'AA', '>flog', 'TT', '>blob', 'TT'])
minimum_counts = 2
self.derep = derep_fulllength.Dereplicator(fasta, minimum_counts)
def setUp(self):
self.fastq = fake_fh('''@lolapolooza\nTAAAACATCATCATCAT\n+lolapolooza\n"#$%&'()*+,-./012\n''')
self.primer = "AAAA"
self.max_primer_diffs = 1
self.primer_remover = util_primer.PrimerRemover(self.fastq, self.primer, self.max_primer_diffs)
def setUp(self):
self.fastq13 = """@lolapolooza:1234#ACGT/1\nAATTAAGTCAAATTTGGCCTGGCCCAGTGTCCAATGTTGT\n+\nABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh\n"""
self.fastq18 = """@lolapolooza:1234#ACGT/1\nAATTAAGTCAAATTTGGCCTGGCCCAGTGTCCAATGTTGT\n+\n"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI\n"""
self.fastq13_fh = fake_fh(self.fastq13 + "\n")
self.fastq13_record = SeqIO.read(self.fastq13_fh, 'fastq')
def test_parse_full_fasta(self):
seq_sid = {'AAA': 'seq0', 'TTT': 'seq4'}
fasta = fake_fh(['>sample=donor1;1', 'AAA', '>sample=donor1;2', 'AAA', '>sample=donor1;3', 'TTT', '>sample=donorT;1', 'TTT'])
abund = index.parse_full_fasta(fasta, seq_sid)
self.assertEqual(abund, {('donor1', 'seq0'): 2, ('donor1', 'seq4'): 1, ('donorT', 'seq4'): 1})
