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from numpy.testing import assert_array_equal
from io import StringIO
from pbcore import data
from pbcore.io.FastqIO import *
# Test QV <-> string conversion routines
class TestQvConversion:
ASCII = (r"""!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`"""
r"""abcdefghijklmnopqrstuvwxyz{|}~""")
QVS = range(0, 94)
def testAsciiFromQvs(self):
assert self.ASCII == asciiFromQvs(self.QVS)
def testQvsFromAscii(self):
assert_array_equal(self.QVS, qvsFromAscii(self.ASCII))
class TestFastqRecord:
HEADER = "chr1|blah|blah\tblah blah"
RC_HEADER = "chr1|blah|blah\tblah blah [revcomp]"
ID = "chr1|blah|blah"
COMMENT = "blah blah"
SEQUENCE = "GATTACA" * 20
RC_SEQUENCE = "TGTAATC" * 20
LENGTH = 140
QUALITY = [10, 11, 12, 13, 14, 15, 16] * 20
RC_QUALITY = [16, 15, 14, 13, 12, 11, 10] * 20
QUALITYSTRING = "+,-./01" * 20
RC_QUALITYSTRING = "10/.-,+" * 20
EXPECTED__STR__ = (
"@chr1|blah|blah\tblah blah\n"
"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATT"
"ACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAG"
"ATTACAGATTACAGATTACA\n"
"+\n"
"+,-./01+,-./01+,-./01+,-./01+,-./01+,-./01+,-./01+,-./01+,-."
"/01+,-./01+,-./01+,-./01+,-./01+,-./01+,-./01+,-./01+,-./01+"
",-./01+,-./01+,-./01")
RC1_EXPECTED__STR__ = (
"@chr1|blah|blah\tblah blah [revcomp]\n"
"TGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTA"
"ATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCT"
"GTAATCTGTAATCTGTAATC\n"
"+\n"
"10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/."
"-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+1"
"0/.-,+10/.-,+10/.-,+")
RC2_EXPECTED__STR__ = (
"@chr1|blah|blah\tblah blah\n"
"TGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTA"
"ATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCT"
"GTAATCTGTAATCTGTAATC\n"
"+\n"
"10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/."
"-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+10/.-,+1"
"0/.-,+10/.-,+10/.-,+")
@classmethod
def setup_class(cls):
cls.record = FastqRecord(cls.HEADER, cls.SEQUENCE, cls.QUALITY)
cls.record2 = FastqRecord(
cls.HEADER, cls.SEQUENCE, qualityString=cls.QUALITYSTRING)
cls.rc1_record = cls.record.reverseComplement()
cls.rc2_record = cls.record.reverseComplement(True)
def test__init__(self):
assert self.HEADER == self.record.header
assert self.SEQUENCE == self.record.sequence
assert self.ID == self.record.id
assert self.COMMENT == self.record.comment
assert_array_equal(self.QUALITY, self.record.quality)
assert self.record == self.record2
def test__str__(self):
assert self.EXPECTED__STR__ == str(self.record)
def test_fromString(self):
recordFromString = FastqRecord.fromString(self.EXPECTED__STR__)
assert self.HEADER == recordFromString.header
assert self.SEQUENCE == recordFromString.sequence
assert_array_equal(self.QUALITY, recordFromString.quality)
def test_reverse_complement1(self):
assert self.rc1_record.header == self.RC_HEADER
assert self.rc1_record.sequence == self.RC_SEQUENCE
assert self.rc1_record.quality == self.RC_QUALITY
assert self.rc1_record.qualityString == self.RC_QUALITYSTRING
assert str(self.rc1_record) == self.RC1_EXPECTED__STR__
def test_reverse_complement2(self):
assert self.rc2_record.header == self.record.header
assert self.rc2_record.sequence == self.RC_SEQUENCE
assert self.rc2_record.quality == self.RC_QUALITY
assert self.rc2_record.qualityString == self.RC_QUALITYSTRING
assert str(self.rc2_record) == self.RC2_EXPECTED__STR__
def test_len(self):
assert self.LENGTH == len(self.record)
assert self.LENGTH == len(self.rc1_record)
assert self.LENGTH == len(self.rc2_record)
def test_eq(self):
header = 'r1'
seq = 'ACGT'
qvs = list(range(10, 10 + len(seq)))
r1 = FastqRecord(header, seq, qvs)
r2 = FastqRecord(header, seq, qvs)
assert r1 == r2
assert not r1 != r2
def test_not_equal(self):
header = 'r1'
seq = 'ACGT'
qvs = list(range(10, 10 + len(seq)))
r1 = FastqRecord(header, seq, qvs)
r2 = FastqRecord('r2', seq, qvs)
assert r1 != r2
class TestFastqReader:
FASTQ1 = StringIO(
"@seq1\n"
"GATTACA\n"
"+\n"
"789:;<=\n")
FASTQ2 = StringIO(
FASTQ1.getvalue() +
"@seq2\n"
"CATTAGA\n"
"+\n"
"@@@@@@@\n")
def test_readFastq1(self):
r1 = FastqReader(self.FASTQ1)
l = list(rec for rec in r1)
assert [FastqRecord("seq1", "GATTACA", range(22, 29))] == l
def test_readFastq2(self):
r2 = FastqReader(self.FASTQ2)
l = list(rec for rec in r2)
assert [FastqRecord("seq1", "GATTACA", range(22, 29)),
FastqRecord("seq2", "CATTAGA", [31]*7)] == l
class TestFastqWriter:
def setup_method(self):
self.fastq1 = StringIO(
"@seq1\n"
"GATTACA\n"
"+\n"
"789:;<=\n")
self.fastq2 = StringIO(
self.fastq1.getvalue() +
"@seq2\n"
"CATTAGA\n"
"+\n"
"@@@@@@@\n")
def test_writeFastq1(self):
f = StringIO()
w = FastqWriter(f)
for record in FastqReader(self.fastq1):
w.writeRecord(record)
assert self.fastq1.getvalue() == f.getvalue()
def test_writeFastq2(self):
f = StringIO()
w = FastqWriter(f)
for record in FastqReader(self.fastq2):
w.writeRecord(record)
assert self.fastq2.getvalue() == f.getvalue()
def test_writeFastq3(self):
f = StringIO()
w = FastqWriter(f)
for record in FastqReader(self.fastq2):
w.writeRecord(record.header, record.sequence, record.quality)
assert self.fastq2.getvalue() == f.getvalue()
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