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fragment fix #101

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merged 3 commits into from
Oct 6, 2024
+4 −7
Merged

fragment fix #101

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6847356
quick bug fix
Koeng101 Oct 6, 2024
9b21549
fix linter issue
Koeng101 Oct 6, 2024
057801b
fix py tests
Koeng101 Oct 6, 2024
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -76,6 +76,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]
- Fixes add flank bug, releases new version of python lib [#101](https://github.com/Koeng101/dnadesign/pull/101)
- Adds feature for adding flanks to RecursiveFragment. [#100](https://github.com/Koeng101/dnadesign/pull/100)
- Adds cloning and recursion functions to python. [#96](https://github.com/Koeng101/dnadesign/pull/96)
- Adds recursive fragmentation. [#92](https://github.com/Koeng101/dnadesign/pull/92)
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6 changes: 1 addition & 5 deletions lib/synthesis/fragment/fragment.go
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Expand Up @@ -291,11 +291,7 @@ func RecursiveFragment(sequence string, maxCodingSizeOligo int, assemblyPattern
if err != nil {
return assembly, err
}
var fragmentsAppended []string
for _, fragment := range fragments {
fragmentsAppended = append(fragmentsAppended, forwardFlank+fragment+reverseFlank)
}
return Assembly{Sequence: sequence, Fragments: fragmentsAppended, Efficiency: efficiency}, nil
return Assembly{Sequence: sequence, Fragments: fragments, Efficiency: efficiency}, nil
}
// After the smallest possible block, begin iterating for each size.
for i, size := range sizes[1:] {
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2 changes: 1 addition & 1 deletion py/setup.py
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Expand Up @@ -13,7 +13,7 @@ def get_shared_lib_ext():

setup(
name='dnadesign',
version='0.1.7',
version='0.1.8',
packages=find_packages(),
package_data={'dnadesign': ['definitions.h', 'libdnadesign.h', "libdnadesign" + get_shared_lib_ext()]},
install_requires=[
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2 changes: 1 addition & 1 deletion py/tests/test_fragment.py
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Expand Up @@ -42,4 +42,4 @@ def test_recursive_fragment():
result = recursive_fragment(gene, max_oligo_len, assembly_pattern, exclude_overhangs, default_overhangs, "GTCTCT", "CGAG")
assert result is not None, "RecursiveFragment failed"
# Add more specific assertions based on the expected structure of the result
assert result.fragments == ['GTCTCTGTCTCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCGAG', 'GTCTCTCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGCGAGCGAG']
assert result.fragments == ['GTCTCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAG', 'CCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGCGAG']
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