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import pytest
from sqt.io.fasta import IndexedFasta, NonIndexedFasta, FastaReader
import os.path
def dpath(path):
return os.path.join(os.path.dirname(__file__), path)
def test_indexedfasta_contextmanager():
with pytest.raises(ValueError):
indfasta = IndexedFasta(dpath("seq.fa"))
with indfasta as ifw:
pass
with indfasta as ifw:
pass
def test_indexedfasta():
for func in IndexedFasta, NonIndexedFasta:
with IndexedFasta(dpath("seq.fa")) as ifa:
assert len(ifa) == 3
chr1 = ifa.get("Chr1")
chr2 = ifa.get("Chr2")
assert chr1[:] == ifa["Chr1"][:]
assert len(chr1) == 1235
assert chr1[0:300].startswith(b'CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATC')
assert chr1[:300].startswith(b'CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATC')
assert chr1[:].startswith(b'CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATC')
assert chr2[227:320] == b'gttggaatcgTTCCGAGTTTTCTCAGCAGTTCTCGGACAAAAACTGATGAATCGTCGAGGAGAATGAGCTTGCCTTGCGTGGGCTGCCATTAG'
assert chr1[:300].startswith(b'CCCTAAACCCTA')
assert chr2[:].endswith(b'TATCCGAGGGATGGTATCGG')
def test_all_regions():
# read the file via a FastaReader, then check that all substrings are equal
path = dpath("indexed.fasta")
sequences = dict()
with FastaReader(path, mode='rb') as fr:
for record in fr:
sequences[record.name.split(' ', 1)[0]] = record.sequence
with IndexedFasta(path):
indexed = IndexedFasta(path)
non_indexed = NonIndexedFasta(path)
regions = []
for name in sorted(sequences):
for i in range(len(sequences[name])):
for j in range(i, len(sequences[name])):
regions.append( (name, i, j) )
for name, start, stop in regions:
expected = sequences[name][start:stop]
assert indexed[name][start:stop] == expected
assert non_indexed[name][start:stop] == expected
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