fragment fix (#101)

fixes a small bug in the recursive fragmenter

README.md

@@ -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)

lib/synthesis/fragment/fragment.go

@@ -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:] {

py/setup.py

@@ -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=[

py/tests/test_fragment.py

@@ -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']