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from pbcore import data
from pbcore.io import FastaReader, FastaWriter, FastaRecord
from io import StringIO
class TestFastaRecord:
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
EXPECTED__STR__ = (
">chr1|blah|blah\tblah blah\n"
"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATT\n"
"ACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAG\n"
"ATTACAGATTACAGATTACA")
RC1_EXPECTED__STR__ = (
">chr1|blah|blah\tblah blah [revcomp]\n"
"TGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTA\n"
"ATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCT\n"
"GTAATCTGTAATCTGTAATC")
RC2_EXPECTED__STR__ = (
">chr1|blah|blah\tblah blah\n"
"TGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTA\n"
"ATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCTGTAATCT\n"
"GTAATCTGTAATCTGTAATC")
@classmethod
def setup_class(cls):
cls.record = FastaRecord(cls.HEADER, cls.SEQUENCE)
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
def test__str__(self):
assert self.EXPECTED__STR__ == str(self.record)
def test_fromString(self):
recordFromString = FastaRecord.fromString(self.EXPECTED__STR__)
assert self.HEADER == recordFromString.header
assert self.SEQUENCE == recordFromString.sequence
def test_reverse_complement1(self):
assert self.rc1_record.header == self.RC_HEADER
assert self.rc1_record.sequence == self.RC_SEQUENCE
assert self.RC1_EXPECTED__STR__ == str(self.rc1_record)
def test_reverse_complement2(self):
assert self.rc2_record.header == self.HEADER
assert self.rc2_record.sequence == self.RC_SEQUENCE
assert self.RC2_EXPECTED__STR__ == str(self.rc2_record)
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'
r1 = FastaRecord(header, seq)
r2 = FastaRecord(header, seq)
assert r1 == r2
def test_not_equal(self):
r1 = FastaRecord('r1', 'ACGT')
r2 = FastaRecord('r2', 'ACGT')
r3 = FastaRecord('r1', 'ACGT')
assert r1 != r2
assert not r1 != r3
class TestFastaReader:
def test_readFasta(self):
f = FastaReader(data.getFasta())
entries = list(f)
assert 48 == len(entries)
assert "ref000001|EGFR_Exon_2" == entries[0].header
assert ("TTTCTTCCAGTTTGCCAAGGCACGAGTAACAAGCTCACGCAGTTGGGCACTTT"
"TGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCAATAACTGTGAGGTGGTCC"
"TTGGGAATTTGGAAATTACCTATGTGCAGAGGAATTATGATCTTTCCTTCTTA"
"AAGGTTGGTGACTTTGATTTTCCT") == entries[0].sequence
def test_dosLineEndingsFasta(self):
f = FastaReader(data.getDosFormattedFasta())
entries = list(f)
for e in entries:
assert "\r" not in e.header
assert 16 == len(e.sequence)
class TestFastaWriter:
def setup_method(self):
self.fasta1 = StringIO(
">chr1|blah|blah\n"
"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATT\n"
"ACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACAG\n"
"ATTACAGATTACAGATTACA\n")
self.fasta2 = StringIO(self.fasta1.getvalue() +
">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 self.fasta1.getvalue() == f.getvalue()
def test_writeFasta2(self):
f = StringIO()
w = FastaWriter(f)
for record in FastaReader(self.fasta2):
w.writeRecord(record.header, record.sequence)
assert self.fasta2.getvalue() == f.getvalue()
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