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import os
import pytest
from pyfaidx import Fasta, Faidx, UnsupportedCompressionFormat, FetchError
from itertools import chain
path = os.path.dirname(__file__)
os.chdir(path)
try:
from Bio import SeqIO
bio = True
except ImportError:
bio = False
@pytest.fixture
def remove_index():
yield
try:
os.remove('data/genes.fasta.gz.fai')
except EnvironmentError:
pass # some tests may delete this file
@pytest.mark.skipif(not bio, reason="Biopython is not installed.")
@pytest.mark.xfail
def test_build_issue_126(remove_index):
""" Samtools BGZF index should be identical to pyfaidx BGZF index """
expect_index = ("gi|563317589|dbj|AB821309.1| 3510 114 70 71\n"
"gi|557361099|gb|KF435150.1| 481 3789 70 71\n"
"gi|557361097|gb|KF435149.1| 642 4368 70 71\n"
"gi|543583796|ref|NR_104216.1| 4573 5141 70 71\n"
"gi|543583795|ref|NR_104215.1| 5317 9901 70 71\n"
"gi|543583794|ref|NR_104212.1| 5374 15415 70 71\n"
"gi|543583788|ref|NM_001282545.1| 4170 20980 70 71\n"
"gi|543583786|ref|NM_001282543.1| 5466 25324 70 71\n"
"gi|543583785|ref|NM_000465.3| 5523 30980 70 71\n"
"gi|543583740|ref|NM_001282549.1| 3984 36696 70 71\n"
"gi|543583738|ref|NM_001282548.1| 4113 40851 70 71\n"
"gi|530384540|ref|XM_005249645.1| 2752 45151 70 71\n"
"gi|530384538|ref|XM_005249644.1| 3004 48071 70 71\n"
"gi|530384536|ref|XM_005249643.1| 3109 51246 70 71\n"
"gi|530384534|ref|XM_005249642.1| 3097 54528 70 71\n"
"gi|530373237|ref|XM_005265508.1| 2794 57830 70 71\n"
"gi|530373235|ref|XM_005265507.1| 2848 60824 70 71\n"
"gi|530364726|ref|XR_241081.1| 1009 63849 70 71\n"
"gi|530364725|ref|XR_241080.1| 4884 65009 70 71\n"
"gi|530364724|ref|XR_241079.1| 2819 70099 70 71\n")
index_file = Faidx('data/genes.fasta.gz').indexname
result_index = open(index_file).read()
assert result_index == expect_index
def test_integer_slice(remove_index):
fasta = Fasta('data/genes.fasta.gz')
expect = fasta['gi|563317589|dbj|AB821309.1|'][:100].seq
result = fasta[0][:100].seq
assert expect == result
def test_integer_index(remove_index):
fasta = Fasta('data/genes.fasta.gz')
expect = fasta['gi|563317589|dbj|AB821309.1|'][100].seq
result = fasta[0][100].seq
assert expect == result
def test_fetch_whole_fasta(remove_index):
expect = [line.rstrip('\n') for line in open('data/genes.fasta') if line[0] != '>']
result = list(chain(*([line for line in record] for record in Fasta('data/genes.fasta.gz', as_raw=True))))
assert expect == result
def test_line_len(remove_index):
fasta = Fasta('data/genes.fasta.gz')
for record in fasta:
assert len(next(iter(record))) == fasta.faidx.index[record.name].lenc
def test_mutable_bgzf(remove_index):
with pytest.raises(UnsupportedCompressionFormat):
fasta = Fasta('data/genes.fasta.gz', mutable=True)
@pytest.mark.xfail(raises=NotImplementedError)
def test_long_names(remove_index):
""" Test that deflines extracted using FastaRecord.long_name are
identical to deflines in the actual file.
"""
deflines = []
with open('data/genes.fasta') as fasta_file:
for line in fasta_file:
if line[0] == '>':
deflines.append(line[1:-1])
fasta = Fasta('data/genes.fasta.gz')
long_names = []
for record in fasta:
long_names.append(record.long_name)
assert deflines == long_names
def test_fetch_whole_entry(remove_index):
faidx = Faidx('data/genes.fasta.gz')
expect = ('ATGACATCATTTTCCACCTCTGCTCAGTGTTCAACATCTGA'
'CAGTGCTTGCAGGATCTCTCCTGGACAAATCAATCAGGTACGACCA'
'AAACTGCCGCTTTTGAAGATTTTGCATGCAGCAGGTGCGCAAGG'
'TGAAATGTTCACTGTTAAAGAGGTCATGCACTATTTAGGTCAGTACAT'
'AATGGTGAAGCAACTTTATGATCAGCAGGAGCAGCATATGGTATATTG'
'TGGTGGAGATCTTTTGGGAGAACTACTGGGACGTCAGAGCTTCTCCGTG'
'AAAGACCCAAGCCCTCTCTATGATATGCTAAGAAAGAATCTTGTCACTTT'
'AGCCACTGCTACTACAGCAAAGTGCAGAGGAAAGTTCCACTTCCAGAAAAA'
'GAACTACAGAAGACGATATCCCCACACTGCCTACCTCAGAGCATAAATGCA'
'TACATTCTAGAGAAGGTGATTGAAGTGGGAAAAAATGATGACCTGGAGGACTC')
result = faidx.fetch('gi|557361099|gb|KF435150.1|',
1, 481)
assert str(result) == expect
def test_fetch_middle(remove_index):
faidx = Faidx('data/genes.fasta.gz')
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'
result = faidx.fetch('gi|557361099|gb|KF435150.1|',
100, 150)
assert str(result) == expect
def test_fetch_end(remove_index):
faidx = Faidx('data/genes.fasta.gz')
expect = 'TC'
result = faidx.fetch('gi|557361099|gb|KF435150.1|',
480, 481)
assert str(result) == expect
def test_fetch_border(remove_index):
""" Fetch past the end of a gene entry """
faidx = Faidx('data/genes.fasta.gz')
expect = 'TC'
with pytest.raises(FetchError):
result = faidx.fetch('gi|557361099|gb|KF435150.1|', 480, 500)
print(result)
assert str(result) == expect
def test_rev(remove_index):
faidx = Faidx('data/genes.fasta.gz')
expect = 'GA'
result = faidx.fetch('gi|557361099|gb|KF435150.1|',
480, 481)
assert str(-result) == expect, result
def test_fetch_past_bounds(remove_index):
""" Fetch past the end of a gene entry """
faidx = Faidx('data/genes.fasta.gz', strict_bounds=True)
with pytest.raises(FetchError):
result = faidx.fetch('gi|557361099|gb|KF435150.1|', 480, 5000)
def test_fetch_negative(remove_index):
""" Fetch starting with a negative coordinate """
faidx = Faidx('data/genes.fasta.gz', strict_bounds=True)
with pytest.raises(FetchError):
result = faidx.fetch('gi|557361099|gb|KF435150.1|', -10, 10)
def test_fetch_reversed_coordinates(remove_index):
""" Fetch starting with a negative coordinate """
faidx = Faidx('data/genes.fasta.gz', strict_bounds=True)
with pytest.raises(FetchError):
result = faidx.fetch('gi|557361099|gb|KF435150.1|', 50, 10)
def test_fetch_keyerror(remove_index):
""" Fetch a key that does not exist """
faidx = Faidx('data/genes.fasta.gz', strict_bounds=True)
with pytest.raises(FetchError):
result = faidx.fetch('gi|joe|gb|KF435150.1|', 1, 10)
def test_blank_string(remove_index):
""" seq[0:0] should return a blank string mdshw5/pyfaidx#53 """
fasta = Fasta('data/genes.fasta.gz', as_raw=True)
assert fasta['gi|557361099|gb|KF435150.1|'][0:0] == ''
def test_slice_from_beginning(remove_index):
fasta = Fasta('data/genes.fasta.gz', as_raw=True)
assert fasta['gi|557361099|gb|KF435150.1|'][:4] == 'ATGA'
def test_slice_from_end(remove_index):
fasta = Fasta('data/genes.fasta.gz', as_raw=True)
assert fasta['gi|557361099|gb|KF435150.1|'][-4:] == 'ACTC'
def test_issue_74_start(remove_index):
f0 = Fasta('data/genes.fasta.gz', one_based_attributes=False)
f1 = Fasta('data/genes.fasta.gz', one_based_attributes=True)
assert f0['gi|557361099|gb|KF435150.1|'][0:90].start == f1['gi|557361099|gb|KF435150.1|'][0:90].start - 1
def test_issue_74_consistency(remove_index):
f0 = Fasta('data/genes.fasta.gz', one_based_attributes=False)
f1 = Fasta('data/genes.fasta.gz', one_based_attributes=True)
assert str(f0['gi|557361099|gb|KF435150.1|'][0:90]) == str(f1['gi|557361099|gb|KF435150.1|'][0:90])
def test_issue_74_end_faidx(remove_index):
f0 = Faidx('data/genes.fasta.gz', one_based_attributes=False)
f1 = Faidx('data/genes.fasta.gz', one_based_attributes=True)
end0 = f0.fetch('gi|557361099|gb|KF435150.1|', 1, 90).end
end1 = f1.fetch('gi|557361099|gb|KF435150.1|', 1, 90).end
assert end0 == end1
def test_issue_74_end_fasta(remove_index):
f0 = Fasta('data/genes.fasta.gz', one_based_attributes=False)
f1 = Fasta('data/genes.fasta.gz', one_based_attributes=True)
end0 = f0['gi|557361099|gb|KF435150.1|'][1:90].end
end1 = f1['gi|557361099|gb|KF435150.1|'][1:90].end
print((end0, end1))
assert end0 == end1
def test_issue_79_fix(remove_index):
f = Fasta('data/genes.fasta.gz')
s = f['gi|557361099|gb|KF435150.1|'][100:105]
print((s.start, s.end))
assert (101, 105) == (s.start, s.end)
def test_issue_79_fix_negate(remove_index):
f = Fasta('data/genes.fasta.gz')
s = f['gi|557361099|gb|KF435150.1|'][100:105]
s = -s
print((s.start, s.end))
assert (105, 101) == (s.start, s.end)
def test_issue_79_fix_one_based_false(remove_index):
f = Fasta('data/genes.fasta.gz', one_based_attributes=False)
s = f['gi|557361099|gb|KF435150.1|'][100:105]
print((s.start, s.end))
assert (100, 105) == (s.start, s.end)
def test_issue_79_fix_one_based_false_negate(remove_index):
f = Fasta('data/genes.fasta.gz', one_based_attributes=False)
s = f['gi|557361099|gb|KF435150.1|'][100:105]
print(s.__dict__)
s = -s
print(s.__dict__)
assert (105, 100) == (s.start, s.end)
def test_fetch_border_padded(remove_index):
""" Fetch past the end of a gene entry """
with pytest.raises(FetchError):
faidx = Faidx('data/genes.fasta.gz', default_seq='N')
expect = 'TCNNNNNNNNNNNNNNNNNNN'
result = faidx.fetch('gi|557361099|gb|KF435150.1|',
480, 500)
print(result)
assert str(result) == expect
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