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import os
import pytest
from pyfaidx import Faidx, Fasta, FetchError
path = os.path.dirname(__file__)
os.chdir(path)
@pytest.fixture
def setup_zero():
with open('data/zero_length.fasta', 'w') as fasta:
fasta.write(""">A
ATCG
>B
>C
>D
GTA
GC""")
yield
os.remove('data/zero_length.fasta')
os.remove('data/zero_length.fasta.fai')
def test_index_zero_length(setup_zero):
fasta = Fasta('data/zero_length.fasta')
def test_fetch_zero_length(setup_zero):
fasta = Fasta('data/zero_length.fasta')
b = fasta["B"]
assert str(b) == ''
@pytest.fixture
def remove_index():
yield
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_as_raw_zero_length_subsequence(remove_index):
fasta = Fasta('data/genes.fasta', as_raw=True, strict_bounds=True)
expect = ''
result = fasta['gi|557361099|gb|KF435150.1|'][100:100]
assert result == expect
def test_zero_length_subsequence(remove_index):
fasta = Fasta('data/genes.fasta', strict_bounds=True)
expect = ''
result = fasta['gi|557361099|gb|KF435150.1|'][100:100]
assert result.seq == expect
def test_fetch_whole_entry(remove_index):
faidx = Faidx('data/genes.fasta')
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')
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')
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')
expect = 'TC'
result = faidx.fetch('gi|557361099|gb|KF435150.1|',
480, 500)
assert str(result) == expect
def test_rev(remove_index):
faidx = Faidx('data/genes.fasta')
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', 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', 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', 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', 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', as_raw=True)
assert fasta['gi|557361099|gb|KF435150.1|'][0:0] == ''
def test_slice_from_beginning(remove_index):
fasta = Fasta('data/genes.fasta', as_raw=True)
assert fasta['gi|557361099|gb|KF435150.1|'][:4] == 'ATGA'
def test_slice_from_end(remove_index):
fasta = Fasta('data/genes.fasta', as_raw=True)
assert fasta['gi|557361099|gb|KF435150.1|'][-4:] == 'ACTC'
def test_issue_74_start(remove_index):
f0 = Fasta('data/genes.fasta', one_based_attributes=False)
f1 = Fasta('data/genes.fasta', 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', one_based_attributes=False)
f1 = Fasta('data/genes.fasta', 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', one_based_attributes=False)
f1 = Faidx('data/genes.fasta', 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', one_based_attributes=False)
f1 = Fasta('data/genes.fasta', 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')
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')
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', 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', 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)
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