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from nose.tools import assert_equal, assert_true, assert_false
from pbcore import data
from pbcore.io import FastaReader, FastaWriter, FastaRecord
from StringIO import StringIO
class TestFastaRecord(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.expected__str__ = (
">chr1|blah|blah\tblah blah\n"
"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATT\n"
"ACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAG\n"
"ATTACAGATTACAGATTACA")
self.rc1_expected__str__ = (
">chr1|blah|blah\tblah blah [revcomp]\n"
"TGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTA\n"
"ATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCT\n"
"GTAATCTGTAATCTGTAATC")
self.rc2_expected__str__ = (
">chr1|blah|blah\tblah blah\n"
"TGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTA\n"
"ATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCT\n"
"GTAATCTGTAATCTGTAATC")
self.record = FastaRecord(self.header, self.sequence)
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)
def test__str__(self):
assert_equal(self.expected__str__, str(self.record))
def test_fromString(self):
recordFromString = FastaRecord.fromString(self.expected__str__)
assert_equal(self.header, recordFromString.header)
assert_equal(self.sequence, recordFromString.sequence)
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_expected__str__, str(self.rc1_record))
def test_reverse_complement2(self):
assert_equal(self.rc2_record.header, self.header)
assert_equal(self.rc2_record.sequence, self.rc_sequence)
assert_equal(self.rc2_expected__str__, str(self.rc2_record))
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'
r1 = FastaRecord(header, seq)
r2 = FastaRecord(header, seq)
assert_true(r1 == r2)
def test_not_equal(self):
r1 = FastaRecord('r1', 'ACGT')
r2 = FastaRecord('r2', 'ACGT')
r3 = FastaRecord('r1', 'ACGT')
assert_true(r1 != r2)
assert_false(r1 != r3)
class TestFastaReader(object):
def test_readFasta(self):
f = FastaReader(data.getFasta())
entries = list(f)
assert_equal(48, len(entries))
assert_equal("ref000001|EGFR_Exon_2", entries[0].header)
assert_equal("TTTCTTCCAGTTTGCCAAGGCACGAGTAACAAGCTCACGCAGTTGGGCACTTT"
"TGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCAATAACTGTGAGGTGGTCC"
"TTGGGAATTTGGAAATTACCTATGTGCAGAGGAATTATGATCTTTCCTTCTTA"
"AAGGTTGGTGACTTTGATTTTCCT",
entries[0].sequence)
def test_dosLineEndingsFasta(self):
f = FastaReader(data.getDosFormattedFasta())
entries = list(f)
for e in entries:
assert_true("\r" not in e.header)
assert_equal(16, len(e.sequence))
class TestFastaWriter(object):
def setup(self):
self.fasta1 = StringIO(
">chr1|blah|blah\n" \
"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATT\n" \
"ACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAG\n" \
"ATTACAGATTACAGATTACA\n")
self.fasta2 = StringIO(self.fasta1.getvalue() + "\n" + \
">chr2|blah|blah\n" \
"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATT\n" \
"ACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAG\n" \
"ATTACAGATTACAGATTACA\n")
def test_writeFasta1(self):
f = StringIO()
w = FastaWriter(f)
for record in FastaReader(self.fasta1):
w.writeRecord(record)
assert_equal(self.fasta1.getvalue(), f.getvalue())
def test_writeFasta2(self):
f = StringIO()
w = FastaWriter(f)
for record in FastaReader(self.fasta1):
w.writeRecord(record.header, record.sequence)
assert_equal(self.fasta1.getvalue(), f.getvalue())
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