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from pbcore import data
from pbcore.io import FastaReader, FastaWriter, IndexedFastaReader
class TestIndexedFastaReader:
FASTAPATH = data.getFasta()
def testIteration(self):
ft = IndexedFastaReader(self.FASTAPATH)
fr = FastaReader(self.FASTAPATH)
ftContigs = list(ft)
frContigs = list(fr)
assert len(frContigs) == len(ftContigs)
assert 48 == len(ftContigs)
for ftC, frC in zip(ftContigs, frContigs):
assert frC.header == ftC.header
assert frC.sequence == ftC.sequence[:]
# Unlike FastaReader, IndexedFastaReader iteration is repeatable.
assert 48 == len(list(ft))
def testAccessByName(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000021 = ft["ref000021|EGFR_Exon_22\tMetadataTest"]
assert "ref000021|EGFR_Exon_22\tMetadataTest" == r000021.header
assert "ref000021|EGFR_Exon_22" == r000021.id
assert "MetadataTest" == r000021.comment
assert ("CACTGCCTCATCTCTCACCATCCCAAGGTGCCTATCAAGTGGATGGCATTGGAATCAATT"
"TTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGTGAGTCATAATCCTGA"
"TGCTAATGAGTTTGTACTGAGGCCAAGCTGG") == r000021.sequence[:]
def testAccessById(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000021 = ft["ref000021|EGFR_Exon_22"]
assert "ref000021|EGFR_Exon_22\tMetadataTest" == r000021.header
assert "ref000021|EGFR_Exon_22" == r000021.id
assert "MetadataTest" == r000021.comment
assert ("CACTGCCTCATCTCTCACCATCCCAAGGTGCCTATCAAGTGGATGGCATTGGAATCAATT"
"TTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGTGAGTCATAATCCTGA"
"TGCTAATGAGTTTGTACTGAGGCCAAGCTGG") == r000021.sequence[:]
def testAccessByPosition(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000001 = ft[0]
assert "<IndexedFastaRecord: ref000001|EGFR_Exon_2>" == repr(r000001)
firstTwo = ft[:2]
assert [ft[0], ft[1]] == firstTwo
lastTwo = ft[-2:]
assert [ft[-2], ft[-1]] == lastTwo
def testSlice(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000021 = ft["ref000021|EGFR_Exon_22"]
sequence = r000021.sequence
assert "CACTGCCTCA" == sequence[0:10]
assert "GCCAAGCTGG" == sequence[-10:]
assert "G" == sequence[-1]
assert "T" == sequence[-3]
assert "C" == sequence[0]
assert "A" == sequence[1]
def test_dosLineEndingsFasta(self):
fr = FastaReader(data.getDosFormattedFasta())
frEntries = list(fr)
ft = IndexedFastaReader(data.getDosFormattedFasta())
ftEntries = list(ft)
assert len(frEntries) == len(ftEntries)
for (frE, ftE) in zip(frEntries, ftEntries):
assert frE.header == ftE.header
assert frE.sequence == ftE.sequence[:]
def test_readWeirdFastaIndex(self):
f = IndexedFastaReader(data.getWeird())
entries = list(f)
assert 1 == len(entries)
assert "chr1" == entries[0].header
assert "acgtacgtacgtact" == entries[0].sequence[:]
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