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Update documentation for get_seq which uses 1-based closed intervals #222

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merged 1 commit into from
Aug 5, 2024

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eroller
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@eroller eroller commented Jul 31, 2024

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@mdshw5
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mdshw5 commented Aug 5, 2024

Good catch! After reviewing my test data (

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
) I agree that the fetch method uses 1-based indices and is end-inclusive.

@mdshw5 mdshw5 merged commit c8652f0 into mdshw5:master Aug 5, 2024
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2 participants