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from nose.tools import assert_equal, assert_true, assert_false
from numpy.testing import assert_array_equal
from pbcore import data
from StringIO import StringIO
from pbcore.io.FastqIO import *
# Test QV <-> string conversion routines
class TestQvConversion(object):
def setup(self):
self.ascii = \
"!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`" + \
"abcdefghijklmnopqrstuvwxyz{|}~"
self.qvs = range(0, 94)
def testAsciiFromQvs(self):
assert_equal(self.ascii, asciiFromQvs(self.qvs))
def testQvsFromAscii(self):
assert_array_equal(self.qvs, qvsFromAscii(self.ascii))
class TestFastqRecord(object):
def setup(self):
self.header = "chr1|blah|blah\tblah blah"
self.rc_header = "chr1|blah|blah\tblah blah [revcomp]"
self.id = "chr1|blah|blah"
self.comment = "blah blah"
self.sequence = "GATTACA" * 20
self.rc_sequence = "TGTAATC" * 20
self.length = 140
self.quality = [10,11,12,13,14,15,16] * 20
self.rc_quality = [16,15,14,13,12,11,10] * 20
self.qualityString = "+,-./01" * 20
self.rc_qualityString = "10/.-,+" * 20
self.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")
self.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/.-,+")
self.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/.-,+")
self.record = FastqRecord(self.header, self.sequence, self.quality)
self.record2 = FastqRecord(self.header, self.sequence,
qualityString=self.qualityString)
self.rc1_record = self.record.reverseComplement()
self.rc2_record = self.record.reverseComplement(True)
def test__init__(self):
assert_equal(self.header, self.record.header)
assert_equal(self.sequence, self.record.sequence)
assert_equal(self.id, self.record.id)
assert_equal(self.comment, self.record.comment)
assert_array_equal(self.quality, self.record.quality)
assert_equal(self.record, self.record2)
def test__str__(self):
assert_equal(self.expected__str__, str(self.record))
def test_fromString(self):
recordFromString = FastqRecord.fromString(self.expected__str__)
assert_equal(self.header, recordFromString.header)
assert_equal(self.sequence, recordFromString.sequence)
assert_array_equal(self.quality, recordFromString.quality)
def test_reverse_complement1(self):
assert_equal(self.rc1_record.header, self.rc_header)
assert_equal(self.rc1_record.sequence, self.rc_sequence)
assert_equal(self.rc1_record.quality, self.rc_quality)
assert_equal(self.rc1_record.qualityString, self.rc_qualityString)
assert_equal(str(self.rc1_record), self.rc1_expected__str__)
def test_reverse_complement2(self):
assert_equal(self.rc2_record.header, self.record.header)
assert_equal(self.rc2_record.sequence, self.rc_sequence)
assert_equal(self.rc2_record.quality, self.rc_quality)
assert_equal(self.rc2_record.qualityString, self.rc_qualityString)
assert_equal(str(self.rc2_record), self.rc2_expected__str__)
def test_len(self):
assert_equal(self.length, len(self.record))
assert_equal(self.length, len(self.rc1_record))
assert_equal(self.length, len(self.rc2_record))
def test_eq(self):
header = 'r1'
seq = 'ACGT'
qvs = list(xrange(10, 10 + len(seq)))
r1 = FastqRecord(header, seq, qvs)
r2 = FastqRecord(header, seq, qvs)
assert_true(r1 == r2)
assert_false(r1 != r2)
def test_not_equal(self):
header = 'r1'
seq = 'ACGT'
qvs = list(xrange(10, 10 + len(seq)))
r1 = FastqRecord(header, seq, qvs)
r2 = FastqRecord('r2', seq, qvs)
assert_true(r1 != r2)
class TestFastqReader(object):
def setup(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_readFastq1(self):
r1 = FastqReader(self.fastq1)
l = list(r1)
assert_equal([FastqRecord("seq1", "GATTACA", range(22, 29))], l)
def test_readFastq2(self):
r2 = FastqReader(self.fastq2)
l = list(r2)
assert_equal([FastqRecord("seq1", "GATTACA", range(22, 29)),
FastqRecord("seq2", "CATTAGA", [31]*7) ],
l)
class TestFastqWriter(object):
def setup(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_equal(self.fastq1.getvalue(), f.getvalue())
def test_writeFastq2(self):
f = StringIO()
w = FastqWriter(f)
for record in FastqReader(self.fastq2):
w.writeRecord(record)
assert_equal(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_equal(self.fastq2.getvalue(), f.getvalue())
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